From pakpoom1 at hotmail.com Fri Sep 1 06:40:38 2006 From: pakpoom1 at hotmail.com (Pakpoom Utta) Date: Thu, 31 Aug 2006 20:40:38 -0800 Subject: [gmx-users] FW: This one is not stoppings itsClimb! Message-ID: From: rktljaouvbarnt at savebig02.comTo: pakpong_jaw at hotmail.comSubject: This one is not stoppings itsClimb!Date: Thu, 31 Aug 2006 04:44:21 +0000 d _________________________________________________________________ Check the weather nationwide with MSN Search: Try it now! http://search.msn.com/results.aspx?q=weather&FORM=WLMTAG -------------- next part -------------- An HTML attachment was scrubbed... URL: From pakpoom1 at hotmail.com Fri Sep 1 06:40:58 2006 From: pakpoom1 at hotmail.com (Pakpoom Utta) Date: Thu, 31 Aug 2006 20:40:58 -0800 Subject: FW: [gmx-users] own forcefield and pairs Message-ID: > Date: Thu, 31 Aug 2006 17:38:37 +0200> From: lists at vrbka.net> To: gmx-users at gromacs.org> Subject: [gmx-users] own forcefield and pairs> > hi guys,> > i have (probably stupid) question, but i'm struggling with it for some > days now without success...> > i want to create a forcefield. everything is ok except the pairs, of > course. the forcefield should be used for simulations with a specific > water model (nada and van der eerden 6 center) - works fine - and some > 'contaminant' - nacl (that's easy) and probably simple aliphatic > alcohols - and here comes the problem.> > relevant excerpts from the topology are pasted at the end (some numbers > are probably wrong, so don't count on the factual correctness of the > potential).> > the alcohol 'strategy' is taken from the ffgmx file (i.e. CH3 as a > single atom). now if i use gen-pairs yes, i guess i shouldn't have the > [pairs] section for the 5OL. with gen-pairs=no, i should probably have > the [pairs] section for all 1-4 interactions. but what values should be > given for the [pairs] section c6 and c12 parameters? the example in > manual (urea) has all zeroes there, however i don't know whether it's > intentional or not.> > funny enough, all 3 possibilities (gen-pairs yes, no [pairs]; gen-pairs > no, [pairs]; gen-pairs no, no [pairs]) give me the same numbers... but > that might be as well as a consequence of the initial structure...> > so i'm confused now and i don't know what setup is the correct one. i > would be really glad if someone could point me in the right direction....> > thanks in advance. best regards,> lubos> > >>>>>>>>>>>>>>> excerpts from the topology follow> > [ defaults ]> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ> 1 2 yes 1.0 1.0> > ;> [ atomtypes ]> ...> ;> ; organic contaminant> ffv_ch2 CH2 14.02700 0.000 A 0.90975E-02 0.35333E-04> ffv_ch3 CH3 15.03500 0.000 A 0.88765E-02 0.26150E-04> ffv_oh OH 15.99940 0.000 A 0.22617E-02 0.15062E-05> ffv_hh HH 1.00800 0.000 A 0.00000E+00 0.00000E+00> > [ moleculetype ]> ; molname nrexcl> 5OL 3> > [ atoms ]> ; id at type res nr resname at name cg nr charge> 1 ffv_hh 1 5OL HH 1 0.398> 2 ffv_oh 1 5OL OH 1 -0.548> 3 ffv_ch2 1 5OL C01 1 0.150> 4 ffv_ch2 1 5OL C02 1 0.000> 5 ffv_ch2 1 5OL C03 1 0.000> 6 ffv_ch2 1 5OL C04 1 0.000> 7 ffv_ch3 1 5OL C05 1 0.000> > [ bonds ]> ; ai aj funct b0 kb> 1 2 1 0.10000 313800.> 2 3 1 0.14300 334720.> 3 4 1 0.15300 334720.> 4 5 1 0.15300 334720.> 5 6 1 0.15300 334720.> 6 7 1 0.15300 334720.> > [ angles ]> ; ai aj ak funct th0 cth> 1 2 3 1 109.500 397.480> 2 3 4 1 109.500 460.240> 3 4 5 1 111.000 460.240> 4 5 6 1 111.000 460.240> 5 6 7 1 111.000 460.240> [ dihedrals ]> ; ai aj ak al funct phi cp mult> 1 2 3 4 1 0.000 1.255 3> 2 3 4 5 1 0.000 5.858 3> 3 4 5 6 1 0.000 5.858 3> 4 5 6 7 1 0.000 5.858 3> > ;[ pairs ]> ; ai aj funct c6 c12> ; 1 4 1 0.0 0.0> ; 1 5 1 0.0 0.0> ; 1 6 1 0.0 0.0> ; 1 7 1 0.0 0.0> ; 2 5 1 0.0 0.0> ; 2 6 1 0.0 0.0> ; 2 7 1 0.0 0.0> ; 3 6 1 0.0 0.0> ; 3 7 1 0.0 0.0> ; 4 7 1 0.0 0.0> > -- > Lubos _ at _"> http://www.lubos.vrbka.net> _______________________________________________> gmx-users mailing list gmx-users at gromacs.org> http://www.gromacs.org/mailman/listinfo/gmx-users> Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org.> Can't post? Read http://www.gromacs.org/mailing_lists/users.php _________________________________________________________________ Search from any Web page with powerful protection. Get the FREE Windows Live Toolbar Today! http://get.live.com/toolbar/overview -------------- next part -------------- An HTML attachment was scrubbed... URL: From dmobley at gmail.com Fri Sep 1 16:50:31 2006 From: dmobley at gmail.com (David Mobley) Date: Fri, 1 Sep 2006 07:50:31 -0700 Subject: [gmx-users] Question about scaling charges In-Reply-To: <20060831190703.69171.qmail@web38804.mail.mud.yahoo.com> References: <1157040508.44f7097cdb288@webmail.cbiot.ufrgs.br> <20060831190703.69171.qmail@web38804.mail.mud.yahoo.com> Message-ID: Arthur, You might want to start by reading something basic on how force fields work, i.e. in Leach's Molecular Modeling book, or maybe Jay Ponder's recent "Force Fields for Protein Simulation" review (available on his web page here: ftp://dasher.wustl.edu/pub/papers/advprotchem-66-27-03.pdf). I am not too sure what you mean by scaling, and the answer to your question probably depends on the force field you want to use. Basically, you need to use charges that are "appropriate" for the force field you are using. For example, it would probably be unwise for me to use, say, some sort of QM with Mulliken analysis to get charges for the partial charges on a ligand to use in a protein for which I use AMBER parameters, since the AMBER partial charges come from SCF 6-31G* RESP fitting, and Mulliken charges won't "match" well since they are very different from what the force field was parameterized with. So, how I would go about answering your question, if I were you, is figure out what force field you plan on using, and then figure out how the "normal" partial charges (i.e. protein partial charges) for that force field were assigned, and then do something similar to get the partial charges for the molecule you are trying to parameterize. You of course need to do something similar with the other parameters, as well. Again, the basic message is that you need to come up with "appropriate" parameters that match well with the force field you are using, which usually means you need to do something similar to what was done to parameterize the force field. David On 8/31/06, Arthur Roberts wrote: > Hi, all, > > I was talking to a friend of mine that works in > an MD lab. He said that the charges from QM/MM or > semiempirical need to be scaled to charges in the > force field. For example, a heme will have specific > charges in the force field, while hemes that represent > different bound states may have a different charge > distribution, depending on which method is used to > calculate it. Let us say that the force field charge > is +1 for simplicity and the charge is +2 by using > other methods. The scaling would suggest that you > would reduce the charge of the heme by one half, so > that it would be compatible to the force field. > However, this doesn't make sense to me, since partial > charges should always be related to an electron and > therefore, in principle, should never have to be > scaled. I would appreciate anyone's input on it. > > Best wishes, > Art > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > From alokjain at iitk.ac.in Fri Sep 1 17:16:47 2006 From: alokjain at iitk.ac.in (alokjain at iitk.ac.in) Date: Fri, 1 Sep 2006 20:46:47 +0530 (IST) Subject: [gmx-users] mdrun_hole problem In-Reply-To: <1156983101.44f6293d27202@webmail.utoronto.ca> References: <1156983101.44f6293d27202@webmail.utoronto.ca> Message-ID: <52711.172.28.124.187.1157123807.squirrel@newwebmail.iitk.ac.in> Dear All, This question is regarding the modified mdrun program i.e mdrun_hole that is used for creating hole in the lipid bilayer to insert a protein into it. When I am trying to run the following command: mdrun_hole -v -hole -holep for_hole.mdp -s run.tpr -o run.trr -x run.xtc -c after_run.gro -g run.log -e run.edr though it appears to be running (i.e. even the top command in linux shows it to be running) but the log file does not show the energy values and stops at the following point: #################################################################### There are 6998 molecules, 16413 charge groups and 34175 atoms There are 0 optimized solvent molecules on node 0 There are 6729 optimized water molecules on node 0 Will do PME sum in reciprocal space. ++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++ U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen {A smooth particle mesh Ewald method J. Chem. Phys. 103 (1995) pp. 8577-8592 -------- -------- --- Thank You --- -------- -------- ######################################################################### Also, I have checked the correctness of the tpr file generated by using simple gromacsv3.1.4 grompp. i.e. when I issue the following command: mdrun -v -s run.tpr -o run.trr -x run.xtc -c after_run.gro -g run.log -e run.edr then it runs properly. Is there any way of checking whether the mdrun_hole has been installed properly (although when I write "mdrun_hole -h", it prints out the hole parameters too, probably telling that mdrun_hole has been installed)? Has anybody ever faced a similar kind of problem with mdrun_hole? kindly suggest me something. waiting for the response, regards, Alok. From Florian.Haberl at chemie.uni-erlangen.de Fri Sep 1 17:55:33 2006 From: Florian.Haberl at chemie.uni-erlangen.de (Florian Haberl) Date: Fri, 1 Sep 2006 17:55:33 +0200 Subject: [gmx-users] mdrun_hole problem In-Reply-To: <52711.172.28.124.187.1157123807.squirrel@newwebmail.iitk.ac.in> References: <1156983101.44f6293d27202@webmail.utoronto.ca> <52711.172.28.124.187.1157123807.squirrel@newwebmail.iitk.ac.in> Message-ID: <200609011755.35441.Florian.Haberl@chemie.uni-erlangen.de> hi, On Friday 01 September 2006 17:16, alokjain at iitk.ac.in wrote: > Dear All, > > This question is regarding the modified mdrun program i.e mdrun_hole that > is used for creating hole in the lipid bilayer to insert a protein into it. > > When I am trying to run the following command: > > mdrun_hole -v -hole -holep for_hole.mdp -s run.tpr -o run.trr -x run.xtc > -c after_run.gro -g run.log -e run.edr > > though it appears to be running (i.e. even the top command in linux shows > it to be running) but the log file does not show the energy values and > stops at the following point: > > #################################################################### > There are 6998 molecules, 16413 charge groups and 34175 atoms > There are 0 optimized solvent molecules on node 0 > There are 6729 optimized water molecules on node 0 > Will do PME sum in reciprocal space. > > ++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++ > U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen > {A smooth particle mesh Ewald method > J. Chem. Phys. 103 (1995) pp. 8577-8592 > -------- -------- --- Thank You --- -------- -------- > ######################################################################### > > Also, I have checked the correctness of the tpr file generated by using > simple gromacsv3.1.4 grompp. i.e. when I issue the following command: > > mdrun -v -s run.tpr -o run.trr -x run.xtc -c after_run.gro -g run.log -e > run.edr > > then it runs properly. > > Is there any way of checking whether the mdrun_hole has been installed > properly (although when I write "mdrun_hole -h", it prints out the hole > parameters too, probably telling that mdrun_hole has been installed)? > Has anybody ever faced a similar kind of problem with mdrun_hole? > kindly suggest me something. have you activated logging? Perhaps set them to nstlog = 1 nstenergy = 1 So every step get logged if this works you can reduce it to normal ones again. Does mdrun generate *.trr file edr ..? > > waiting for the response, > regards, > Alok. > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Greetings, Florian -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) ? 9131 ? 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- From singh at biophysik.chemie.uni-dortmund.de Fri Sep 1 18:56:11 2006 From: singh at biophysik.chemie.uni-dortmund.de (singh) Date: Fri, 1 Sep 2006 18:56:11 +0200 Subject: [gmx-users] opls Message-ID: Dear Users, I am trying to simulate a capped pentapeptide using OPLS force field. Pdb2gmx runs successfully , however grompp gives following warnings WARNING 1 [file "topol.top", line 632]: No default Ryckaert-Bell. types, using zeroes WARNING 2 [file "topol.top", line 857]: No default Ryckaert-Bell. types, using zeroes How should I proceed if these parameters are missing in OPLS. The topology and gro files are attached herewith Regards, Gurpreet ------------------------------------------------- University of Dortmund Department of Chemistry Physical Chemistry I - Biophysical Chemistry Otto-Hahn Str. 6 D-44227 Dortmund Germany Office: C1-06 room 176 Phone: +49 231 755 3916 ------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: topol.top Type: application/octet-stream Size: 28494 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: conf.gro Type: application/octet-stream Size: 4347 bytes Desc: not available URL: From singh at biophysik.chemie.uni-dortmund.de Fri Sep 1 19:31:09 2006 From: singh at biophysik.chemie.uni-dortmund.de (singh) Date: Fri, 1 Sep 2006 19:31:09 +0200 Subject: [gmx-users] opls Message-ID: Dear Users, I am trying to simulate a capped pentapeptide using OPLS force field. Pdb2gmx runs successfully , however grompp gives following warnings WARNING 1 [file "topol.top", line 632]: No default Ryckaert-Bell. types, using zeroes WARNING 2 [file "topol.top", line 857]: No default Ryckaert-Bell. types, using zeroes How should I proceed if these parameters are missing in OPLS. ------------------------------------------------- University of Dortmund Department of Chemistry Physical Chemistry I - Biophysical Chemistry Otto-Hahn Str. 6 D-44227 Dortmund Germany Office: C1-06 room 176 Phone: +49 231 755 3916 ------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From leafyoung81-group at yahoo.com Fri Sep 1 19:57:50 2006 From: leafyoung81-group at yahoo.com (Yang Ye) Date: Sat, 02 Sep 2006 01:57:50 +0800 Subject: [gmx-users] opls In-Reply-To: References: Message-ID: <44F8749E.2030007@yahoo.com> Check your topology file against ffoplsaa.rtp and ffoplsaabon.itp Yang Ye singh wrote: > > Dear Users, > > I am trying to simulate a capped pentapeptide using OPLS force field. > Pdb2gmx runs successfully , however grompp gives following warnings > > WARNING 1 [file "topol.top", line 632]: > > No default Ryckaert-Bell. types, using zeroes > > WARNING 2 [file "topol.top", line 857]: > > No default Ryckaert-Bell. types, using zeroes > > > > How should I proceed if these parameters are missing in OPLS. > > The topology and gro files are attached herewith > > > > Regards, > > Gurpreet > > ------------------------------------------------- > > University of Dortmund > Department of Chemistry > Physical Chemistry I - Biophysical Chemistry > Otto-Hahn Str. 6 > D-44227 Dortmund > Germany > > Office: C1-06 room 176 > Phone: +49 231 755 3916 > > ------------------------------------------------- > > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php From fileti at iq.usp.br Fri Sep 1 20:38:17 2006 From: fileti at iq.usp.br (Eudes Fileti) Date: Fri, 1 Sep 2006 15:38:17 -0300 Subject: [gmx-users] Internal coordinates to the topology Message-ID: <65e289a20609011138q1d21d0fdn12dc423db3c80313@mail.gmail.com> Dear gmx users I have a crystalline cell with 150 atoms. Somebody would know to say me as to generate the pairs (bond), triple (angles) and quaternios (dihedrals) for the archive top? I already used PRODRG but I have not sucess... Thanks in advance. eef ______________________________________ Eudes Eterno Fileti Centro de Ci?ncia Naturais e Humanas Universidade Federal do ABC Rua Santa Ad?lia, 166 CEP 09210-170 skype: eefileti -------------- next part -------------- An HTML attachment was scrubbed... URL: From fileti at iq.usp.br Fri Sep 1 20:42:51 2006 From: fileti at iq.usp.br (Eudes Fileti) Date: Fri, 1 Sep 2006 15:42:51 -0300 Subject: [gmx-users] Internal coordinates to the topology Message-ID: <65e289a20609011142p6ef228c6je495553a5d823de@mail.gmail.com> Dear gmx-user I have a crystalline cell with 150 atoms. Somebody would know to say me as to generate the pairs (bond), triples (angles) and quaternios (dihedral) for the topology? Is there a good program to do this? For smaller molecules the Gaussian works fine but in this case its fails. I already used PRODRG but I have not sucess... Thanks in advance eef ______________________________________ Eudes Eterno Fileti Centro de Ci?ncia Naturais e Humanas Universidade Federal do ABC Rua Santa Ad?lia, 166 CEP 09210-170 skype: eefileti -------------- next part -------------- An HTML attachment was scrubbed... URL: From ababakha at mccammon.ucsd.edu Fri Sep 1 22:19:44 2006 From: ababakha at mccammon.ucsd.edu (Arneh Babakhani) Date: Fri, 01 Sep 2006 13:19:44 -0700 Subject: [gmx-users] g_msd Message-ID: <44F895E0.9060009@mccammon.ucsd.edu> Hi everyone, quick question about g_msd, When I execute: *g_msd -f FullMD1.trr -s FullMD1.tpr -n ForDiffusion.ndx -o test -lateral z* At the end, the following is outputted in my terminal: *D[ Protein] 0.1207 (+/- 0.0847) 1e-5 cm^2/s* My index file only contains one group, labeled Protein. So is this number, *0.1207*, the MSD of the entire group Protein? Or is this the average (over the atoms) MSD in the group Protein? (I think the latter is the case, b/c in the manual, it's stated that g_msd computes the MSD of atoms . . . just double-checking). Thanks much, Arneh -------------- next part -------------- An HTML attachment was scrubbed... URL: From spoel at xray.bmc.uu.se Fri Sep 1 22:58:45 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Fri, 01 Sep 2006 22:58:45 +0200 Subject: [gmx-users] g_msd In-Reply-To: <44F895E0.9060009@mccammon.ucsd.edu> References: <44F895E0.9060009@mccammon.ucsd.edu> Message-ID: <44F89F05.2070200@xray.bmc.uu.se> Arneh Babakhani wrote: > Hi everyone, quick question about g_msd, > > When I execute: *g_msd -f FullMD1.trr -s FullMD1.tpr -n > ForDiffusion.ndx -o test -lateral z* > > At the end, the following is outputted in my terminal: > > *D[ Protein] 0.1207 (+/- 0.0847) 1e-5 cm^2/s* > > My index file only contains one group, labeled Protein. So is this > number, *0.1207*, the MSD of the entire group Protein? Or is this the > average (over the atoms) MSD in the group Protein? (I think the latter > is the case, b/c in the manual, it's stated that g_msd computes the MSD > of atoms . . . just double-checking). it is the average. for something as large as a protein you would prefer to have the center-of-mass diffusion. This is not implemented unfortunately. > > Thanks much, > > Arneh > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From quimico69 at yahoo.com Sat Sep 2 02:16:41 2006 From: quimico69 at yahoo.com (Victor Manuel Rosas-Garcia) Date: Fri, 1 Sep 2006 17:16:41 -0700 (PDT) Subject: [gmx-users] box of water with ions Message-ID: <20060902001641.81749.qmail@web53504.mail.yahoo.com> Hello everybody, I'm trying to build a water box with some calcium carbonate in it but, for the life of me, I cannot get it right. I can build a box of water with CaCl without any problems. I have a grompp.mdp file and then: genbox -box 2 2 2 -cs spc216 -o h2o.gro pdb2gmx -f h2o.gro -q h2o.pdb -n index.ndx grompp -f grompp.mdp -c h2o.gro -n index.ndx -p topol.top -o topol.tpr mdrun -v genion -s topol.tpr -o out.gro -pname Ca -pq 2 -np 5 -nname Cl -nq -1 -nn 10 and then pdb2gmx... mdrun... No problem there. I am aware that genion cannot introduce polyatomic ions so, to generate a box of water with CaCO3 I tried to introduce the anion first with genbox and then the Ca with genion (I have CO2(-2) as a pdb file): genbox -box 2 2 2 -cs spc216 -ci co3.pdb -nmol 10 pdb2gmx -f out.gro -q out.pdb -n index.ndx and I got the following error message: [snip, snip] ------------------------------------------------------- Program pdb2gmx, VERSION 3.3 Source code file: resall.c, line: 438 Fatal error: Residue 'DRG' not found in residue topology database ------------------------------------------------------- So, I tried x2top: x2top -f out.gro -o topol.top and then I got [snip, snip] ------------------------------------------------------- Program x2top, VERSION 3.3 Source code file: futil.c, line: 537 Fatal error: Library file ffG43a1.n2t not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) ------------------------------------------------------- so, neither pdb2gmx nor x2top worked. I submitted CO3(-2) to the prodrg server and I have all the files, but it gave me SIX *.TOP files so, I don't really know which one to use. None of them seem (to me) to fit the format of the gromacs topology files I saw in the gromacs documentation. Needless to say, I am FAR from being an experienced gromacs user, although I do have experience in computational chemistry, just not molecular dynamics. Any recommendations? Victor M. Rosas Garc?a, PhD Coordinador del Posgrado en Ciencias Facultad de Ciencias Quimicas, UANL e-mail: quimico69 at yahoo.com Tel: (81) 8329-4010 ext. 6253 Fax: (81) 8376-5375 __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From aroberts99163 at yahoo.com Sat Sep 2 02:44:27 2006 From: aroberts99163 at yahoo.com (Arthur Roberts) Date: Fri, 1 Sep 2006 17:44:27 -0700 (PDT) Subject: [gmx-users] Making small molecule topology files In-Reply-To: Message-ID: <20060902004427.40405.qmail@web38815.mail.mud.yahoo.com> Hi, all, I would like to make a small molecule using the OPLSAA force field. Is there a simple way to do it (i.e. a program that makes the topology file) or do I have to manually type the OPLSAA topology file? Thank you in advance, Art From zgxjlx at gmail.com Sat Sep 2 05:13:33 2006 From: zgxjlx at gmail.com (liu xin) Date: Sat, 2 Sep 2006 11:13:33 +0800 Subject: [gmx-users] Simulation problem with extended membrane system! Message-ID: Dear GMX-users: I met a problem when doing simulation with the membrane , here's what I've done so far: I download the dppc128.pdb file and dppc.top files from Dr. Tielman's website, equilibrated this dppc128 system for 10ns, I checked the final structure with VMD, everything seemed ok. Then I extended this system to a larger one with thicker water layers and more lipid molecules with the following commands: editconf -f dppc128.pdb -o dppc128_center.pdb -center 0 0 4.1 genbox -cs dppc128_center.pdb -o larger_box.pdb -box 9.2 9.2 8.3 So I got a membrane system with 183 lipid molecules and 12752 SOL molecules, then I did a simulation with this system for 1ns. But when I check the final structure, I find the water molecules, at the edge of the box, spread across the Z axis, but not insert into the lipid molecules. It seems that the water molecules are all around the lipid molecules in a cubic box. At the same time, I find the arrangement of the lipid molecules are disordered, the lipid leaflets get closer, and become crooked, not as straight as before. It looks like that the whole system is compressed across the Z axis. And what's weird to me is that if I don't extend the water, make the two water layers as thick as before, just extend the dppc128 system to a dppc183 system, then doing simulation, there is no such phenomenon. Is it because I've got too much water? Or is there something wrong with my method? Here's my mdout.mdp file: ; VARIOUS PREPROCESSING OPTIONS title = DPPC ; Preprocessor - specify a full path if necessary. cpp = /lib/cpp include = define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit = 0 dt = 0.002 nsteps = 500000 ; For exact run continuation or redoing part of a run init_step = 0 ; mode for center of mass motion removal comm-mode = Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps = ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol = 10 emstep = 0.01 ; Max number of iterations in relax_shells niter = 20 ; Step size (ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr = 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 2500 nstvout = 1000 nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint = 1000 ; Output frequency for energies to log file and energy file nstlog = 1000 nstenergy = 1000 ; Output frequency and precision for xtc file nstxtcout = 0 xtc-precision = 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = SOL DPPC ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist = 1.0 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.0 ; Relative dielectric constant for the medium and the reaction field epsilon_r = 1 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 1.0 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Seperate tables between energy group pairs energygrp_table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = yes ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = berendsen ; Groups to couple separately tc-grps = SOL DPPC ; Time constant (ps) and reference temperature (K) tau_t = 0.1 0.1 ref_t = 300 300 ; Pressure coupling Pcoupl = berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Random seed for Andersen thermostat andersen_seed = 815131 ; OPTIONS FOR QMMM calculations QMMM = no ; Groups treated Quantum Mechanically QMMM-grps = ; QM method QMmethod = ; QMMM scheme QMMMscheme = normal ; QM basisset QMbasis = ; QM charge QMcharge = ; QM multiplicity QMmult = ; Surface Hopping SH = ; CAS space options CASorbitals = CASelectrons = SAon = SAoff = SAsteps = ; Scale factor for MM charges MMChargeScaleFactor = 1 ; Optimization of QM subsystem bOPT = bTS = ; SIMULATED ANNEALING ; Type of annealing for each temperature group (no/single/periodic) annealing = ; Number of time points to use for specifying annealing in each group annealing_npoints = ; List of times at the annealing points for each group annealing_time = ; Temp. at each annealing point, for each group. annealing_temp = ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 300.0 gen_seed = 173529 ; OPTIONS FOR BONDS constraints = all-bonds ; Type of constraint algorithm constraint-algorithm = Lincs ; Do not constrain the start configuration unconstrained-start = no ; Use successive overrelaxation to reduce the number of shake iterations Shake-SOR = no ; Relative tolerance of shake shake-tol = 1e-04 ; Highest order in the expansion of the constraint coupling matrix lincs-order = 4 ; Number of iterations in the final step of LINCS. 1 is fine for ; normal simulations, but use 2 to conserve energy in NVE runs. ; For energy minimization with constraints it should be 4 to 8. lincs-iter = 1 ; Lincs will write a warning to the stderr if in one step a bond ; rotates over more degrees than lincs-warnangle = 30 ; Convert harmonic bonds to morse potentials morse = no ; ENERGY GROUP EXCLUSIONS ; Pairs of energy groups for which all non-bonded interactions are excluded energygrp_excl = ; NMR refinement stuff ; Distance restraints type: No, Simple or Ensemble disre = No ; Force weighting of pairs in one distance restraint: Conservative or Equal disre-weighting = Conservative ; Use sqrt of the time averaged times the instantaneous violation disre-mixed = no disre-fc = 1000 disre-tau = 0 ; Output frequency for pair distances to energy file nstdisreout = 100 ; Orientation restraints: No or Yes orire = no ; Orientation restraints force constant and tau for time averaging orire-fc = 0 orire-tau = 0 orire-fitgrp = ; Output frequency for trace(SD) and S to energy file nstorireout = 100 ; Dihedral angle restraints: No, Simple or Ensemble dihre = No dihre-fc = 1000 dihre-tau = 0 ; Output frequency for dihedral values to energy file nstdihreout = 100 ; Free energy control stuff free-energy = no init-lambda = 0 delta-lambda = 0 sc-alpha = 0 sc-power = 0 sc-sigma = 0.3 ; Non-equilibrium MD stuff acc-grps = accelerate = freezegrps = freezedim = cos-acceleration = 0 deform = ; Electric fields ; Format is number of terms (int) and for all terms an amplitude (real) ; and a phase angle (real) E-x = E-xt = E-y = E-yt = E-z = E-zt = ; User defined thingies user1-grps = user2-grps = userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 Any suggestion is appreciated! -------------- next part -------------- An HTML attachment was scrubbed... URL: From spoel at xray.bmc.uu.se Sat Sep 2 10:00:13 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Sat, 02 Sep 2006 10:00:13 +0200 Subject: [gmx-users] box of water with ions In-Reply-To: <20060902001641.81749.qmail@web53504.mail.yahoo.com> References: <20060902001641.81749.qmail@web53504.mail.yahoo.com> Message-ID: <44F93A0D.9070303@xray.bmc.uu.se> Victor Manuel Rosas-Garcia wrote: > Hello everybody, > > I'm trying to build a water box with some calcium carbonate in it but, for the > life of me, I cannot get it right. I can build a box of water with CaCl > without any problems. I have a grompp.mdp file and then: > > genbox -box 2 2 2 -cs spc216 -o h2o.gro > pdb2gmx -f h2o.gro -q h2o.pdb -n index.ndx > grompp -f grompp.mdp -c h2o.gro -n index.ndx -p topol.top -o topol.tpr > mdrun -v > genion -s topol.tpr -o out.gro -pname Ca -pq 2 -np 5 -nname Cl -nq -1 -nn 10 > > and then pdb2gmx... mdrun... No problem there. you shoulnd't use pdb2gmx for other stuff than proteins. check chapter 5 in the manual > > I am aware that genion cannot introduce polyatomic ions so, to generate a box > of water with CaCO3 I tried to introduce the anion first with genbox and then > the Ca with genion (I have CO2(-2) as a pdb file): > > genbox -box 2 2 2 -cs spc216 -ci co3.pdb -nmol 10 > pdb2gmx -f out.gro -q out.pdb -n index.ndx > > and I got the following error message: > [snip, snip] > ------------------------------------------------------- > Program pdb2gmx, VERSION 3.3 > Source code file: resall.c, line: 438 > > Fatal error: > Residue 'DRG' not found in residue topology database > > ------------------------------------------------------- > > So, I tried x2top: > x2top -f out.gro -o topol.top > > and then I got > [snip, snip] > ------------------------------------------------------- > Program x2top, VERSION 3.3 > Source code file: futil.c, line: 537 > > Fatal error: > Library file ffG43a1.n2t not found in current dir nor in default directories. > (You can set the directories to search with the GMXLIB path variable) > ------------------------------------------------------- > > so, neither pdb2gmx nor x2top worked. I submitted CO3(-2) to the prodrg server > and I have all the files, but it gave me SIX *.TOP files so, I don't really > know which one to use. None of them seem (to me) to fit the format of the > gromacs topology files I saw in the gromacs documentation. Needless to say, I > am FAR from being an experienced gromacs user, although I do have experience in > computational chemistry, just not molecular dynamics. > > Any recommendations? > > > > Victor M. Rosas Garc?a, PhD > Coordinador del Posgrado en Ciencias > Facultad de Ciencias Quimicas, UANL > e-mail: quimico69 at yahoo.com > Tel: (81) 8329-4010 ext. 6253 > Fax: (81) 8376-5375 > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From spoel at xray.bmc.uu.se Sat Sep 2 10:01:04 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Sat, 02 Sep 2006 10:01:04 +0200 Subject: [gmx-users] Making small molecule topology files In-Reply-To: <20060902004427.40405.qmail@web38815.mail.mud.yahoo.com> References: <20060902004427.40405.qmail@web38815.mail.mud.yahoo.com> Message-ID: <44F93A40.4030405@xray.bmc.uu.se> Arthur Roberts wrote: > Hi, all, > > I would like to make a small molecule using the > OPLSAA force field. Is there a simple way to do it > (i.e. a program that makes the topology file) or do I > have to manually type the OPLSAA topology file? you can use prodrg for a start, or use the x2top version that is in 3.3 cvs. > > Thank you in advance, > Art > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From alokjain at iitk.ac.in Sat Sep 2 11:19:38 2006 From: alokjain at iitk.ac.in (alokjain at iitk.ac.in) Date: Sat, 2 Sep 2006 14:49:38 +0530 (IST) Subject: [gmx-users] mdrun_hole problem In-Reply-To: <200609011755.35441.Florian.Haberl@chemie.uni-erlangen.de> References: <1156983101.44f6293d27202@webmail.utoronto.ca> <52711.172.28.124.187.1157123807.squirrel@newwebmail.iitk.ac.in> <200609011755.35441.Florian.Haberl@chemie.uni-erlangen.de> Message-ID: <4716.172.26.116.101.1157188778.squirrel@newwebmail.iitk.ac.in> Thanks Florian, As you have replied, Yes I had activated logging (that means I had the molsurf_log option in "for_hole.mdp" file . But it is not creating my specified log file and also the normal *.log file in run.mdp file) As you had suggested I just tried with nstlog = 1 (previously it was 100) nstenergy = 1 But still it is not printing any energy values in log file,even for zeros step. It is creating *.log *.edr files but not *.trr file, but in the *.edr file nothing is there. Can you suggest me , how I can overcome this problem? Best regards, Alok > hi, > > On Friday 01 September 2006 17:16, alokjain at iitk.ac.in wrote: >> Dear All, >> >> This question is regarding the modified mdrun program i.e mdrun_hole >> that >> is used for creating hole in the lipid bilayer to insert a protein into >> it. >> >> When I am trying to run the following command: >> >> mdrun_hole -v -hole -holep for_hole.mdp -s run.tpr -o run.trr -x run.xtc >> -c after_run.gro -g run.log -e run.edr >> >> though it appears to be running (i.e. even the top command in linux >> shows >> it to be running) but the log file does not show the energy values and >> stops at the following point: >> >> #################################################################### >> There are 6998 molecules, 16413 charge groups and 34175 atoms >> There are 0 optimized solvent molecules on node 0 >> There are 6729 optimized water molecules on node 0 >> Will do PME sum in reciprocal space. >> >> ++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++ >> U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. >> Pedersen >> {A smooth particle mesh Ewald method >> J. Chem. Phys. 103 (1995) pp. 8577-8592 >> -------- -------- --- Thank You --- -------- -------- >> ######################################################################### >> >> Also, I have checked the correctness of the tpr file generated by using >> simple gromacsv3.1.4 grompp. i.e. when I issue the following command: >> >> mdrun -v -s run.tpr -o run.trr -x run.xtc -c after_run.gro -g run.log -e >> run.edr >> >> then it runs properly. >> >> Is there any way of checking whether the mdrun_hole has been installed >> properly (although when I write "mdrun_hole -h", it prints out the hole >> parameters too, probably telling that mdrun_hole has been installed)? >> Has anybody ever faced a similar kind of problem with mdrun_hole? >> kindly suggest me something. > > have you activated logging? > Perhaps set them to > > nstlog = 1 > nstenergy = 1 > > So every step get logged if this works you can reduce it to normal ones > again. > Does mdrun generate *.trr file edr ..? > >> >> waiting for the response, >> regards, >> Alok. >> >> _______________________________________________ >> gmx-users mailing list gmx-users at gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-request at gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > Greetings, > > Florian > > -- > ------------------------------------------------------------------------------- > Florian Haberl > Computer-Chemie-Centrum > Universitaet Erlangen/ Nuernberg > Naegelsbachstr 25 > D-91052 Erlangen > Telephone: +49(0) ??? 9131 ??? 85 26581 > Mailto: florian.haberl AT chemie.uni-erlangen.de > ------------------------------------------------------------------------------- > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > From singh at biophysik.chemie.uni-dortmund.de Sat Sep 2 14:36:08 2006 From: singh at biophysik.chemie.uni-dortmund.de (singh) Date: Sat, 2 Sep 2006 14:36:08 +0200 Subject: [gmx-users] RE: opls In-Reply-To: <20060901210506.2AF802407C@xray.bmc.uu.se> Message-ID: Hi, I have checked both the files. These lines corresponds to following dihedrals in my topology Dihedral (1-5-7-9) 1 opls_135 1 ACE CH3 1 -0.18 12.011 ; qtot -0.18 5 opls_235 1 ACE C 2 0.5 12.011 ; qtot 0.5 7 opls_238 2 PHE N 3 -0.5 14.0067 ; qtot -0.5 9 opls_224B 2 PHE CA 3 0.14 12.011 ; qtot -0.06 And (81-88-90-92) 81 opls_224B 6 SER CA 30 0.14 12.011 ; qtot -0.06 88 opls_235 6 SER C 33 0.5 12.011 ; qtot 0.5 90 opls_238 7 NAC N 34 -0.5 14.0067 ; qtot -0.5 92 opls_242 7 NAC CH3 35 0.02 12.011 ; qtot -0.18 In rtp file all the atomtypes are there in corresponding residues however in ffoplsaabon.itp, I could not find an entry in dihedral types for these dihedrals. Regards, Gurpreet Singh Check your topology file against ffoplsaa.rtp and ffoplsaabon.itp Yang Ye singh wrote: > > Dear Users, > > I am trying to simulate a capped pentapeptide using OPLS force field. > Pdb2gmx runs successfully , however grompp gives following warnings > > WARNING 1 [file "topol.top", line 632]: > > No default Ryckaert-Bell. types, using zeroes > > WARNING 2 [file "topol.top", line 857]: > > No default Ryckaert-Bell. types, using zeroes > > > > How should I proceed if these parameters are missing in OPLS. > > The topology and gro files are attached herewith > > > > Regards, > > Gurpreet > > ------------------------------------------------- > > University of Dortmund > Department of Chemistry > Physical Chemistry I - Biophysical Chemistry > Otto-Hahn Str. 6 > D-44227 Dortmund > Germany > > Office: C1-06 room 176 > Phone: +49 231 755 3916 > From dong at pampas.chem.purdue.edu Sat Sep 2 17:08:18 2006 From: dong at pampas.chem.purdue.edu (Dongsheng Zhang) Date: Sat, 02 Sep 2006 11:08:18 -0400 Subject: [gmx-users] RE: opls In-Reply-To: References: Message-ID: <1157209698.20547.4.camel@pampas.chem.purdue.edu> Hello, I believe this question has been asked several times. It is true that ffoplsaabon.itp misses some parameters for dihedral for the capped residues (ACE NAC). I think you can add some estimated values to the ffoplsaabon.itp, or ignore the warnings. All the best! Donnsheng On Sat, 2006-09-02 at 14:36 +0200, singh wrote: > > > > Hi, > I have checked both the files. These lines corresponds to following > dihedrals in my topology > > Dihedral (1-5-7-9) > 1 opls_135 1 ACE CH3 1 -0.18 12.011 ; qtot > -0.18 > 5 opls_235 1 ACE C 2 0.5 12.011 ; qtot > 0.5 > 7 opls_238 2 PHE N 3 -0.5 14.0067 ; qtot > -0.5 > 9 opls_224B 2 PHE CA 3 0.14 12.011 ; qtot > -0.06 > > And (81-88-90-92) > 81 opls_224B 6 SER CA 30 0.14 12.011 ; > qtot -0.06 > 88 opls_235 6 SER C 33 0.5 12.011 ; > qtot 0.5 > 90 opls_238 7 NAC N 34 -0.5 14.0067 ; > qtot -0.5 > 92 opls_242 7 NAC CH3 35 0.02 12.011 ; > qtot -0.18 > In rtp file all the atomtypes are there in corresponding residues however in > ffoplsaabon.itp, I could not find an entry in dihedral types for these > dihedrals. > > Regards, > Gurpreet Singh > > > > > > > > > Check your topology file against ffoplsaa.rtp and ffoplsaabon.itp > > Yang Ye > > singh wrote: > > > > Dear Users, > > > > I am trying to simulate a capped pentapeptide using OPLS force field. > > Pdb2gmx runs successfully , however grompp gives following warnings > > > > WARNING 1 [file "topol.top", line 632]: > > > > No default Ryckaert-Bell. types, using zeroes > > > > WARNING 2 [file "topol.top", line 857]: > > > > No default Ryckaert-Bell. types, using zeroes > > > > > > > > How should I proceed if these parameters are missing in OPLS. > > > > The topology and gro files are attached herewith > > > > > > > > Regards, > > > > Gurpreet > > > > ------------------------------------------------- > > > > University of Dortmund > > Department of Chemistry > > Physical Chemistry I - Biophysical Chemistry > > Otto-Hahn Str. 6 > > D-44227 Dortmund > > Germany > > > > Office: C1-06 room 176 > > Phone: +49 231 755 3916 > > > > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php From spoel at xray.bmc.uu.se Mon Sep 4 08:49:52 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Mon, 04 Sep 2006 08:49:52 +0200 Subject: [gmx-users] [Fwd: gen_seed GROMACS] Message-ID: <44FBCC90.4090303@xray.bmc.uu.se> -------- Original Message -------- Subject: gen_seed GROMACS Date: Sun, 3 Sep 2006 19:36:35 -0700 (PDT) From: Fenghui Fan To: spoel at xray.bmc.uu.se Will you please give me an explaination on gen_seed? How can we decide its value? How does it influence the final resuts? What is getpid? I am looking forward to getting your reply. Best regards. Fenghui Fan __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From spoel at xray.bmc.uu.se Mon Sep 4 08:52:44 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Mon, 04 Sep 2006 08:52:44 +0200 Subject: [gmx-users] [Fwd: gen_seed GROMACS] In-Reply-To: <44FBCC90.4090303@xray.bmc.uu.se> References: <44FBCC90.4090303@xray.bmc.uu.se> Message-ID: <44FBCD3C.3050509@xray.bmc.uu.se> David van der Spoel wrote: > > > -------- Original Message -------- > Subject: gen_seed GROMACS > Date: Sun, 3 Sep 2006 19:36:35 -0700 (PDT) > From: Fenghui Fan > To: spoel at xray.bmc.uu.se > > Will you please give me an explaination on gen_seed? > How can we decide its value? How does it influence the > final resuts? What is getpid? > > I am looking forward to getting your reply. > > Best regards. > > Fenghui Fan > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > It's a random number seed. You will get different velocities with a different seed. That's all. try: man getpid -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From Mark.Abraham at anu.edu.au Mon Sep 4 08:56:23 2006 From: Mark.Abraham at anu.edu.au (Mark Abraham) Date: Mon, 04 Sep 2006 16:56:23 +1000 Subject: [gmx-users] [Fwd: gen_seed GROMACS] In-Reply-To: <44FBCC90.4090303@xray.bmc.uu.se> References: <44FBCC90.4090303@xray.bmc.uu.se> Message-ID: <44FBCE17.2080305@anu.edu.au> David van der Spoel wrote: > > > -------- Original Message -------- > Subject: gen_seed GROMACS > Date: Sun, 3 Sep 2006 19:36:35 -0700 (PDT) > From: Fenghui Fan > To: spoel at xray.bmc.uu.se > > Will you please give me an explaination on gen_seed? > How can we decide its value? How does it influence the > final resuts? What is getpid? See section 7.3.16 in the manual. Mark From anwar at cdfd.org.in Mon Sep 4 14:35:49 2006 From: anwar at cdfd.org.in (anwar at cdfd.org.in) Date: Mon, 4 Sep 2006 05:35:49 -0700 (PDT) Subject: [gmx-users] invacuo simulation Message-ID: <28254133.1157343805966.JavaMail.nobody@sunserver> Dear gmx users, I am working on protein invacuo simulation in different condition like considering different box size (0.7, 0.8, 1.0) and also with and without pressure coupling. When I am looking at the rmsd and gyration results, they are all varying alot for all the simulations. The simulation seem to be equilibrated for a certain time and then but again they start deviating. I dont have any clue for why the system is showing a lot of discrepancies with in different simulations when they differ only in the box size. Can some on through some light on it? regards Anwar ---------------------- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 anwar.m1 at gmail.com ----------------------- - From jiqing at iccas.ac.cn Mon Sep 4 09:20:20 2006 From: jiqing at iccas.ac.cn (=?gb2312?B?1vfUwiCjuqOp?=) Date: Mon, 4 Sep 2006 15:20:20 +0800 Subject: [gmx-users] Tip5p with gromos 96, error atom has mass 0 Message-ID: <000f01c6cff2$94c1c540$851ae29f@jiqing> Hi all: I built a topol file for tip5p water accordint to tip5p.itp which is designed for OPLS.But when i used grompp to built a tpr file, three errors came even the system just have one tip5p water. The error is : ERROR 1 [file "topol.top", line 10]: atom OW has mass 0 ERROR 2 [file "topol.top", line 10]: atom HW1 has mass 0 ERROR 3 [file "topol.top", line 10]: atom HW2 has mass 0 In fact, the mass for all above atoms were all defined in atp file. How can i fix it? Thanks a lot. The build steps are follows: 1. Named the atom type in new tip5p.itp. Add them to ffG53a6.atp and ffG53a6nb.itp. In tip5p.itp: [ atoms ] ; id at type res nr residu name at name cg nr charge 1 5p_O 1 SOL OW 1 0 2 5p_H 1 SOL HW1 1 0.241 3 5p_H 1 SOL HW2 1 0.241 4 5p_L 1 SOL OL1 1 -0.241 5 5p_L 1 SOL OL2 1 -0.241 In ffG53a6.atp 5p_O 15.99940 ; O TIP5P Water 5p_H 1.00800 ; H TIP5P Water 5p_L 0.00000 ; L TIP5P Water In ffG53a6nb.itp 5p_O 8 0.000 0.000 A 2.470013e-03 2.278383e-06 5p_H 1 0.000 0.000 A 0 0 5p_L 0 0.000 0.000 D 0 0 2. Write top file. #include "ffG53a6.itp" #include "tip5p_.itp" [ system ] ; Name Protein [ molecules ] ; Compound #mols SOL 1 3. Built gro 5 1SOL OW 1 0.321 1.614 0.603 1SOL HW1 2 0.377 1.643 0.675 1SOL HW2 3 0.258 1.555 0.645 1SOL OL1 4 0.358 1.581 0.554 1SOL OL2 5 0.288 1.669 0.574 0.5 0.5 0.5 4. grompp -f em.mdp Then the errors came. ************************************************* Ji Qing Institute of Chemistry, Chinese Academy of Sciences Tel: 0086-10-62562894 ?82618423 ************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From spoel at xray.bmc.uu.se Mon Sep 4 09:22:23 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Mon, 04 Sep 2006 09:22:23 +0200 Subject: [gmx-users] Tip5p with gromos 96, error atom has mass 0 In-Reply-To: <000f01c6cff2$94c1c540$851ae29f@jiqing> References: <000f01c6cff2$94c1c540$851ae29f@jiqing> Message-ID: <44FBD42F.9070802@xray.bmc.uu.se> ?? ?? wrote: > Hi all: > I built a topol file for tip5p water accordint to tip5p.itp which is > designed for OPLS.But when i used grompp to built a tpr file, three > errors came even the system just have one tip5p water. > > The error is : > > ERROR 1 [file "topol.top", line 10]: > atom OW has mass 0 > ERROR 2 [file "topol.top", line 10]: > atom HW1 has mass 0 > ERROR 3 [file "topol.top", line 10]: > atom HW2 has mass 0 > > In fact, the mass for all above atoms were all defined in atp file. How > can i fix it? Thanks a lot. > > The build steps are follows: > 1. Named the atom type in new tip5p.itp. Add them to ffG53a6.atp and > ffG53a6nb.itp. > In tip5p.itp: > [ atoms ] > ; id at type res nr residu name at name cg nr charge > 1 5p_O 1 SOL OW 1 0 > 2 5p_H 1 SOL HW1 1 0.241 > 3 5p_H 1 SOL HW2 1 0.241 > 4 5p_L 1 SOL OL1 1 -0.241 > 5 5p_L 1 SOL OL2 1 -0.241 > In ffG53a6.atp > 5p_O 15.99940 ; O TIP5P Water > 5p_H 1.00800 ; H TIP5P Water > 5p_L 0.00000 ; L TIP5P Water > In ffG53a6nb.itp > 5p_O 8 0.000 0.000 A 2.470013e-03 2.278383e-06 > 5p_H 1 0.000 0.000 A 0 0 > 5p_L 0 0.000 0.000 D 0 0 > > 2. Write top file. > #include "ffG53a6.itp" > #include "tip5p_.itp" > > [ system ] > ; Name > Protein > > [ molecules ] > ; Compound #mols > SOL 1 > > 3. Built gro > > 5 > 1SOL OW 1 0.321 1.614 0.603 > 1SOL HW1 2 0.377 1.643 0.675 > 1SOL HW2 3 0.258 1.555 0.645 > 1SOL OL1 4 0.358 1.581 0.554 > 1SOL OL2 5 0.288 1.669 0.574 > 0.5 0.5 0.5 > 4. grompp -f em.mdp > > Then the errors came. > > > ************************************************* > Ji Qing > Institute of Chemistry, Chinese Academy of Sciences > Tel: 0086-10-62562894 ?82618423 > ************************************************* > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php put the mass in your tip5p.itp file. -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From Florian.Haberl at chemie.uni-erlangen.de Mon Sep 4 10:26:40 2006 From: Florian.Haberl at chemie.uni-erlangen.de (Florian Haberl) Date: Mon, 4 Sep 2006 10:26:40 +0200 Subject: [gmx-users] analyses of g_hbond Message-ID: <200609041026.40556.Florian.Haberl@chemie.uni-erlangen.de> Hi, has someone written a script for analyses output of g_hbond. I'm searching for a tool which calculates ratio of hbond to analysis time, and also converts atom nr to atom names. I know only some lines in perl, but if someone has done it, some work has been saved. Greetings, Florian -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) ? 9131 ? 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- From Florian.Haberl at chemie.uni-erlangen.de Mon Sep 4 11:40:02 2006 From: Florian.Haberl at chemie.uni-erlangen.de (Florian Haberl) Date: Mon, 4 Sep 2006 11:40:02 +0200 Subject: [gmx-users] amber ff and cpp error message Message-ID: <200609041140.02907.Florian.Haberl@chemie.uni-erlangen.de> Hi, i got a strange behaviour of amberff implementation in gromacs (http://folding.stanford.edu/ffamber/): cpp is not running without problems or warnings: checking input for internal consistency... calling /lib/cpp... In file included from /raid1/haberl/bin/gmx/amb_gmx/share/gromacs/top/ffamber03.itp:19, from topol.top:11: /raid1/haberl/bin/gmx/amb_gmx/share/gromacs/top/ffamber03bon.itp:538:22: warning: missing whitespace after the macro name /raid1/haberl/bin/gmx/amb_gmx/share/gromacs/top/ffamber03bon.itp:540:22: warning: missing whitespace after the macro name /raid1/haberl/bin/gmx/amb_gmx/share/gromacs/top/ffamber03bon.itp:541:22: warning: missing whitespace after the macro name /raid1/haberl/bin/gmx/amb_gmx/share/gromacs/top/ffamber03bon.itp:544:21: warning: missing whitespace after the macro name /raid1/haberl/bin/gmx/amb_gmx/share/gromacs/top/ffamber03bon.itp:555:19: warning: missing whitespace after the macro name processing topology... This are the lines from the error or warning message, i would say "*, ' " produces them. ; missing nucleic torsions #define proper_X_CT_N*_X 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 #define proper_X_CM_CT_X 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 #define proper_X_CK_N*_X 14.22560 0.00000 -14.22560 0.00000 0.00000 0.00000 #define proper_X_CB_N*_X 13.80720 0.00000 -13.80720 0.00000 0.00000 0.00000 #define proper_X_CA_NC_X 40.16640 0.00000 -40.16640 0.00000 0.00000 0.00000 #define proper_X_CQ_NC_X 56.90240 0.00000 -56.90240 0.00000 0.00000 0.00000 is this a normal behaviour? OS is suse 10.1 running on x86_64 cpp -v Using built-in specs. Target: x86_64-suse-linux Configured with: ../configure --enable-threads=posix --prefix=/usr --with-local-prefix=/usr/local --infodir=/usr/share/info --mandir=/usr/share/man --libdir=/usr/lib64 --libexecdir=/usr/lib64 --enable-languages=c,c++,objc,fortran,java,ada --enable-checking=release --with-gxx-include-dir=/usr/include/c++/4.1.0 --enable-ssp --disable-libssp --enable-java-awt=gtk --enable-gtk-cairo --disable-libjava-multilib --with-slibdir=/lib64 --with-system-zlib --enable-shared --enable-__cxa_atexit --enable-libstdcxx-allocator=new --without-system-libunwind --with-cpu=generic --host=x86_64-suse-linux Thread model: posix gcc version 4.1.0 (SUSE Linux) /usr/lib64/gcc/x86_64-suse-linux/4.1.0/cc1 -E -quiet -v - -mtune=generic #include "..." search starts here: #include <...> search starts here: /usr/local/include /usr/lib64/gcc/x86_64-suse-linux/4.1.0/include /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/include /usr/include End of search list Greetings, Florian -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) ? 9131 ? 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- From Florian.Haberl at chemie.uni-erlangen.de Mon Sep 4 11:48:38 2006 From: Florian.Haberl at chemie.uni-erlangen.de (Florian Haberl) Date: Mon, 4 Sep 2006 11:48:38 +0200 Subject: [gmx-users] amber ff and cpp error message In-Reply-To: <200609041140.02907.Florian.Haberl@chemie.uni-erlangen.de> References: <200609041140.02907.Florian.Haberl@chemie.uni-erlangen.de> Message-ID: <200609041148.39092.Florian.Haberl@chemie.uni-erlangen.de> On Monday 04 September 2006 11:40, Florian Haberl wrote: > Hi, > > i got a strange behaviour of amberff implementation in gromacs > (http://folding.stanford.edu/ffamber/): > > cpp is not running without problems or warnings: is in faq as e.sorin mailed me http://folding.stanford.edu/ffamber/FAQ.html#grompp > > checking input for internal consistency... > calling /lib/cpp... > In file included > from /raid1/haberl/bin/gmx/amb_gmx/share/gromacs/top/ffamber03.itp:19, > from topol.top:11: > /raid1/haberl/bin/gmx/amb_gmx/share/gromacs/top/ffamber03bon.itp:538:22: > warning: missing whitespace after the macro name > /raid1/haberl/bin/gmx/amb_gmx/share/gromacs/top/ffamber03bon.itp:540:22: > warning: missing whitespace after the macro name > /raid1/haberl/bin/gmx/amb_gmx/share/gromacs/top/ffamber03bon.itp:541:22: > warning: missing whitespace after the macro name > /raid1/haberl/bin/gmx/amb_gmx/share/gromacs/top/ffamber03bon.itp:544:21: > warning: missing whitespace after the macro name > /raid1/haberl/bin/gmx/amb_gmx/share/gromacs/top/ffamber03bon.itp:555:19: > warning: missing whitespace after the macro name > processing topology... > > This are the lines from the error or warning message, i would say "*, ' " > produces them. > > ; missing nucleic torsions > #define proper_X_CT_N*_X 0.00000 0.00000 0.00000 0.00000 > 0.00000 0.00000 > #define proper_X_CM_CT_X 0.00000 0.00000 0.00000 0.00000 > 0.00000 0.00000 > #define proper_X_CK_N*_X 14.22560 0.00000 -14.22560 0.00000 > 0.00000 0.00000 > #define proper_X_CB_N*_X 13.80720 0.00000 -13.80720 0.00000 > 0.00000 0.00000 > #define proper_X_CA_NC_X 40.16640 0.00000 -40.16640 0.00000 > 0.00000 0.00000 > #define proper_X_CQ_NC_X 56.90240 0.00000 -56.90240 0.00000 > 0.00000 0.00000 > > is this a normal behaviour? > > OS is suse 10.1 running on x86_64 > > cpp -v > Using built-in specs. > Target: x86_64-suse-linux > Configured with: ../configure --enable-threads=posix --prefix=/usr > --with-local-prefix=/usr/local --infodir=/usr/share/info > --mandir=/usr/share/man --libdir=/usr/lib64 --libexecdir=/usr/lib64 > --enable-languages=c,c++,objc,fortran,java,ada --enable-checking=release > --with-gxx-include-dir=/usr/include/c++/4.1.0 --enable-ssp --disable-libssp > --enable-java-awt=gtk --enable-gtk-cairo --disable-libjava-multilib > --with-slibdir=/lib64 --with-system-zlib --enable-shared > --enable-__cxa_atexit --enable-libstdcxx-allocator=new > --without-system-libunwind --with-cpu=generic --host=x86_64-suse-linux > Thread model: posix > gcc version 4.1.0 (SUSE Linux) > /usr/lib64/gcc/x86_64-suse-linux/4.1.0/cc1 -E -quiet -v - -mtune=generic > #include "..." search starts here: > #include <...> search starts here: > /usr/local/include > /usr/lib64/gcc/x86_64-suse-linux/4.1.0/include > > /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/includ >e /usr/include > End of search list > > Greetings, > > Florian -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) ? 9131 ? 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- From alokjain at iitk.ac.in Mon Sep 4 13:09:08 2006 From: alokjain at iitk.ac.in (alokjain at iitk.ac.in) Date: Mon, 4 Sep 2006 16:39:08 +0530 (IST) Subject: [gmx-users] mdrun_hole problem again Message-ID: <3402.172.26.116.101.1157368148.squirrel@newwebmail.iitk.ac.in> Dear All, two days back I posted a question regarding mdrun-hole but my problem has still not ben solved,so I am writing it again in more elaborate form. I appreciate any comment on my procedure. In sort my problem is, I am not getting any output from modified mdrun_hole program. Here are the series of steps I follow. 1) First I took well equilibrated pope.pdb file from Dr. Peter tieleman site. 2) I align my protein with respect to pope bilayer by using editconf. 3)I used make_hole.pl script (comes with modified mdrun program..thanks to Dr. Grahm smith) to make a hole,by following command make_hole.pl -f inbilayer.pdb -o outbilayer.pdb -r 1.5 -lipat P8 -lipid POPE it created the hole of my desired size.I visualized the output pdb file, it was visible. 4)I used GRASP and generated the molecular surface of my protein by the procedure describe in the tutorial . 5) I used normal grompp and generated the run.tpr file.I used following command grompp -v -f run.mdp -po run_out -c outbilayer.pdb -r outbilayer.pdb -p test.top -o run.tpr my test.top file ############################# test.top ############################### ; topology for a pure POPE bilayer with 340 lipids and 6729 SPC water ; molecules #include "/home/gromds/alok/membrane-protein/ffgmx.itp" #include "/home/gromds/alok/membrane-protein/pope.itp" #ifdef FLEX_SPC #include "flexspc.itp" #else #include "spc.itp" #endif [ system ] ; name Pure POPE bilayer with 340 lipids and 6729 water molecules [ molecules ] ; name number POPE 340 SOL 6729 ###################################################################### my run.mdp file looks like it.... ############################ run.mdp ################################# define = -DPOSRES_LIPID -DFLEX_SPC integrator = md dt = 0.002 nsteps = 50000 nstxout = 50 nstvout = 50 nstlog = 5 nstenergy = 25 nstxtcout = 25 xtc_grps = POPE SOL energygrps = POPE SOL nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 vdw-type = Cut-off tcoupl = Berendsen tc-grps = POPE SOL tau_t = 0.1 0.1 ref_t = 300 300 Pcoupl = Berendsen tau_p = 10 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp = 300 gen_seed = 173529 constraints = all-bonds #################################################################### 6) Finally I tried to run modified mdrun_hole program. It seems to run (I checked by top command), but it is not giving me any output. It generated *.log (but no energy value, noe even for zeroth time), *.edr (0kb) ...and no *.trr, *.xtc, *.gro files. I am using following command. mdrun_modified -v -s run.tpr -o run.trr -x run.xtc -c after_run.gro -e run.edr -g run.log -hole -holep for_hole.mdp I checked validity of my run.tpr file by running it in normal mdrun (3.1.4) it was running fine.. my for_hole.mdp files as follows. ###########################3## for_hole.mdp ############################ holetype = Grasp_ascii hfm = 10 molsurf_file = /home/gromds/alok/membrane-protein/out sofs = 0 hp1 = 1 hp2 = 17680 supf = 10 resforces = yes molsurf_log = /home/gromds/alok/membrane-protein/test.log debugsurf = yes sfm = 10.0 s1 = 17681 s2 = 37867 hz = 3.0 hz1 = 0 hz2 = 6.0 ####################################################################### I tried with debugsurf = yes and no option but no success, even it does not produce molsurfpdb.pdb & insidesurf.pdb file with yes option. please suggest me somthing. I am stuck at this point. Thanks a lot, Alok From qiaobf at gmail.com Mon Sep 4 15:50:29 2006 From: qiaobf at gmail.com (Qiao Baofu) Date: Mon, 4 Sep 2006 15:50:29 +0200 Subject: [gmx-users] Question about angle constraints In-Reply-To: <44F5A844.40105@xray.bmc.uu.se> References: <6a91f07b0608300714l6126e0b3vb9b44dd14ac9f71a@mail.gmail.com> <44F5A844.40105@xray.bmc.uu.se> Message-ID: <6a91f07b0609040650w12beb075l483c074a9a2f8b40@mail.gmail.com> Hi David, I think maybe the virtual site is suitable for NO3-. But how about PF6-? Please see the .itp file for the PF6-, which is wroten by myself. 1. Because all the bond-length are constrainted, there is no energy term in the .itp file. Therefore it is not a problem of energy term, I think. 2. Except the bond-length, the angles F-P-F should be constrainted to be 90 or 180. *********** .itp file********************* [ moleculetype ] ; Name PF6- PFN 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 opls_977 1 PFN PAA 1 1.34 30.97376 2 opls_978 1 PFN FAA1 1 -0.39 18.99840 3 opls_978 1 PFN FAA2 1 -0.39 18.99840 4 opls_978 1 PFN FAA3 1 -0.39 18.99840 5 opls_978 1 PFN FAA4 1 -0.39 18.99840 6 opls_978 1 PFN FAA5 1 -0.39 18.99840 7 opls_978 1 PFN FAA6 1 -0.39 18.99840 [ constraints ] 1 2 1 0.1560 1 3 1 0.1560 1 4 1 0.1560 1 5 1 0.1560 1 6 1 0.1560 1 7 1 0.1560 ; The structure of PF6- is Octahedral [ constraints ] 2 3 2 0.2206 2 4 2 0.2206 2 5 2 0.3120 2 6 2 0.2206 2 7 2 0.2206 3 4 2 0.2206 3 5 2 0.2206 3 6 2 0.3120 3 7 2 0.2206 4 5 2 0.2206 4 6 2 0.2206 4 7 2 0.3120 5 6 2 0.2206 5 7 2 0.2206 6 7 2 0.2206 ******************* .top file****************** ;the force field files to be included #include "ffoplsaa.itp" ; include the PF6- topology #include "PFN.itp" [ system ] PFN [ molecules ] ; molecule name number PFN 5 **************************************** 2006/8/30, David van der Spoel : > > Qiao Baofu wrote: > > Hi All, > > > > In my simulation, the NO3- is used, in which the three N-O bond length > > is constraints. And a planar triangular structure is used. > > I used the type "1" of [ constraints ] to constraint the bond length. > > Because I only find angle constraints which is used on H-involved > angles, > > I used the type "2" of [ constraints ] to constraint the length between > > Os. (The distance is calculated from the triangular structure). After > > the Energy Minimization, all the bong length become very long (much > > bigger than the box length). Who knows how to solve it? > > > > You probably have an error in the topology. Check energy terms. > > However, you probably should consider modeling this using either an > improper dihedral to keep the N in the plane or, if you want to keep the > molecule planar at every time use a virtual site representation for the N. > > > Sincerely yours, > > Baofu Qiao, PhD > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users mailing list gmx-users at gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-request at gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Sincerely yours, Baofu Qiao, PhD -------------- next part -------------- An HTML attachment was scrubbed... URL: From spoel at xray.bmc.uu.se Mon Sep 4 15:59:28 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Mon, 04 Sep 2006 15:59:28 +0200 Subject: [gmx-users] Question about angle constraints In-Reply-To: <6a91f07b0609040650w12beb075l483c074a9a2f8b40@mail.gmail.com> References: <6a91f07b0608300714l6126e0b3vb9b44dd14ac9f71a@mail.gmail.com> <44F5A844.40105@xray.bmc.uu.se> <6a91f07b0609040650w12beb075l483c074a9a2f8b40@mail.gmail.com> Message-ID: <44FC3140.4070305@xray.bmc.uu.se> Qiao Baofu wrote: > Hi David, > > I think maybe the virtual site is suitable for NO3-. But how about > PF6-? Please see the .itp file for the PF6-, which is wroten by myself. > 1. Because all the bond-length are constrainted, there is no energy > term in the .itp file. Therefore it is not a problem of energy term, I > think. > 2. Except the bond-length, the angles F-P-F should be constrainted to be > 90 or 180. this may work, just try it. However, be careful that the number of degrees of freedom is correct, that is it won't be correct! You will have to adapt the temperature in your simulation to match it. > > *********** .itp file********************* > [ moleculetype ] > ; Name PF6- > PFN 3 > > [ atoms ] > ; nr type resnr resid atom cgnr charge mass > 1 opls_977 1 PFN PAA 1 1.34 30.97376 > 2 opls_978 1 PFN FAA1 1 -0.39 18.99840 > 3 opls_978 1 PFN FAA2 1 -0.39 18.99840 > 4 opls_978 1 PFN FAA3 1 - 0.39 18.99840 Typo on the above line... > 5 opls_978 1 PFN FAA4 1 -0.39 18.99840 > 6 opls_978 1 PFN FAA5 1 -0.39 18.99840 > 7 opls_978 1 PFN FAA6 1 -0.39 18.99840 > > [ constraints ] > 1 2 1 0.1560 > 1 3 1 0.1560 > 1 4 1 0.1560 > 1 5 1 0.1560 > 1 6 1 0.1560 > 1 7 1 0.1560 > > ; The structure of PF6- is Octahedral > [ constraints ] > 2 3 2 0.2206 > 2 4 2 0.2206 > 2 5 2 0.3120 > 2 6 2 0.2206 > 2 7 2 0.2206 > 3 4 2 0.2206 > 3 5 2 0.2206 > 3 6 2 0.3120 > 3 7 2 0.2206 > 4 5 2 0.2206 > 4 6 2 0.2206 > 4 7 2 0.3120 > 5 6 2 0.2206 > 5 7 2 0.2206 > 6 7 2 0.2206 > > ******************* .top file****************** > ;the force field files to be included > #include "ffoplsaa.itp" > > > ; include the PF6- topology > #include "PFN.itp" > > [ system ] > PFN > > [ molecules ] > ; molecule name number > PFN 5 > **************************************** > > > 2006/8/30, David van der Spoel >: > > Qiao Baofu wrote: > > Hi All, > > > > In my simulation, the NO3- is used, in which the three N-O bond > length > > is constraints. And a planar triangular structure is used. > > I used the type "1" of [ constraints ] to constraint the bond length. > > Because I only find angle constraints which is used on H-involved > angles, > > I used the type "2" of [ constraints ] to constraint the length > between > > Os. (The distance is calculated from the triangular structure). > After > > the Energy Minimization, all the bong length become very long (much > > bigger than the box length). Who knows how to solve it? > > > > You probably have an error in the topology. Check energy terms. > > However, you probably should consider modeling this using either an > improper dihedral to keep the N in the plane or, if you want to keep the > molecule planar at every time use a virtual site representation for > the N. > > > Sincerely yours, > > Baofu Qiao, PhD > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users mailing list gmx-users at gromacs.org > > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-request at gromacs.org > . > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > spoel at xray.bmc.uu.se > spoel at gromacs.org > http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org > . > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > Sincerely yours, > Baofu Qiao, PhD > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From choique_pacifico at yahoo.com Mon Sep 4 18:51:34 2006 From: choique_pacifico at yahoo.com (Ariel Alvarez) Date: Mon, 4 Sep 2006 16:51:34 +0000 (GMT) Subject: [gmx-users] AFM pulling Message-ID: <20060904165134.53881.qmail@web30301.mail.mud.yahoo.com> Is there anyone who can tell me what are the 10 colums in my pull.pdo. The first is time. And the others? I can't find this information in the manual. It says that pull.pdo contains the calculated forces. Are the rest of the colums the coordinates of the forces pulling each atom of the molecule? (I'm pulling water molecules). Thank you a lot. Ariel --------------------------------- Pregunt?. Respond?. Descubr?. Todo lo que quer?as saber, y lo que ni imaginabas, est? en Yahoo! Respuestas (Beta). Probalo ya! -------------- next part -------------- An HTML attachment was scrubbed... URL: From spoel at xray.bmc.uu.se Mon Sep 4 19:03:40 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Mon, 04 Sep 2006 19:03:40 +0200 Subject: [gmx-users] invacuo simulation In-Reply-To: <28254133.1157343805966.JavaMail.nobody@sunserver> References: <28254133.1157343805966.JavaMail.nobody@sunserver> Message-ID: <44FC5C6C.7020702@xray.bmc.uu.se> anwar at cdfd.org.in wrote: > Dear gmx users, > I am working on protein invacuo simulation in different condition like > considering different box size (0.7, 0.8, 1.0) and also with and without > pressure coupling. When I am looking at the rmsd and gyration results, > they are all varying alot for all the simulations. > The simulation seem to be equilibrated for a certain time and then but > again they start deviating. I dont have any clue for why the system is > showing a lot of discrepancies with in different simulations when they > differ only in the box size. Can some on through some light on it? > regards pressure coupling does not make sense in vacuum, because there is no box. If you want to use PBC and a box anyway the size doesn't matter except that the molecule should not see it's own image. > Anwar > > ---------------------- > Mohd Anwaruddin > Project Assistant > C/o DR.H.A.Nagarajaram > Lab of Computational Biology and Bioinformatics > Center for DNA Fingerprinting and Diagnostics(CDFD) > Nacharam > Hyderabad-500 076 > INDIA. > Tel: +91-8413-235467,68,69,70 ext 2019 > anwar.m1 at gmail.com > ----------------------- > > > > - > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From ewalton at MIT.EDU Mon Sep 4 21:20:37 2006 From: ewalton at MIT.EDU (Emily Walton) Date: Mon, 4 Sep 2006 15:20:37 -0400 Subject: [gmx-users] AFM pulling In-Reply-To: <20060904165843.1140A24083@xray.bmc.uu.se> References: <20060904165843.1140A24083@xray.bmc.uu.se> Message-ID: <03D70588-FF6A-4192-BF03-5344AACDE764@mit.edu> From a few months ago: > Hi, > > I posted the following message a few weeks ago and just noticed that > I was wrong. The column order is actually: > > Time, Ref. X, Ref. Y, Ref. Z, Pull X, Spring X, Pull Y, Spring Y, > Pull Z, Spring Z > > > Not intuitive, but it does make it very easy to make sure your spring > starts in the same position as your pull group :) > > This doesn't change anything about my script, so those of you who > have it, don't worry, the script is right. It was just an error in > the previous post. > > -Emily Walton You can search the mailing list archives at: http://www.gromacs.org/ external/search.html -Emily Walton > Message: 4 > Date: Mon, 4 Sep 2006 16:51:34 +0000 (GMT) > From: Ariel Alvarez > Subject: [gmx-users] AFM pulling > To: Lista GMX-Users > Message-ID: <20060904165134.53881.qmail at web30301.mail.mud.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Is there anyone who can tell me what are the 10 colums in my > pull.pdo. The first is time. And the others? I can't find this > information in the manual. It says that pull.pdo contains the > calculated forces. Are the rest of the colums the coordinates of > the forces pulling each atom of the molecule? (I'm pulling water > molecules). Thank you a lot. Ariel > > --------------------------------- > Pregunt?. Respond?. Descubr?. > Todo lo que quer?as saber, y lo que ni imaginabas, > est? en Yahoo! Respuestas (Beta). > Probalo ya! > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.gromacs.org/pipermail/gmx-users/attachments/ > 20060904/bdcbb651/attachment.html > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > > > End of gmx-users Digest, Vol 29, Issue 9 > **************************************** From muc176 at psu.edu Mon Sep 4 20:20:11 2006 From: muc176 at psu.edu (MURAT CETINKAYA) Date: Mon, 4 Sep 2006 14:20:11 -0400 Subject: [gmx-users] AFM pull and ensembles Message-ID: <1157394010l.454724l.0l@psu.edu> Hi all, I have two questions about PMF calculations. 1) Which one is more suggested for an AFM pull simulation, an NVT or an NPT ensemble? I am trying both vacuo and solvated runs (with OPLS-AA ff). 2) My second question is about solvation: I found out that pulling action is much smoother in solvent than in vacuo. It may be bad to have energy and rms jumps in vacuo. On the other hand, I think it would be better for estimating forces and energy differences with an abrupt change in the system. What is you opinion about effects of solvation? Thanks in advance Murat Cetinkaya -------------- next part -------------- An HTML attachment was scrubbed... URL: From chris.neale at utoronto.ca Tue Sep 5 00:48:16 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Mon, 4 Sep 2006 18:48:16 -0400 Subject: [gmx-users] Simulation problem with extended membrane system! Message-ID: <1157410096.44fcad30a63f9@webmail.utoronto.ca> It is unclear why your second method works for you. However, given that it does, just use genbox -cs spc216.gro -cp 183_system_that_worked.gro -box 9.2 9.2 8.3 and then use your own script to remove any spc waters that were put inside the membrane and modify the nubers in your topology file accordingly. I imagine that your first attempt didn't work since an entire dppc molecule is removed upon a single collision and this will lead to "holes" in your membrane that will quickly fill with water. Of course this should also have happened in your second attempt... I am not sure what was different there. You need semiisotropic pressure coupling and you need to stop every once and a while and remove any water molecules that are inside the membrane. Note that isotropic Pcoupling in a membrane system (as you have been doing) has the potential to provide a surface tension (or the opposite) that you have not been intentionally including and so you can expect your membrane to behave differently. Chris. From chris.neale at utoronto.ca Tue Sep 5 01:05:03 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Mon, 4 Sep 2006 19:05:03 -0400 Subject: [gmx-users] mdrun_hole problem again Message-ID: <1157411103.44fcb11f690ef@webmail.utoronto.ca> - you didn't do an energy minimization - you used hz1 0 and I used hz1 1.0 - you didn't include make hole options hr,hx,hy *** Somebody already suggested nstlog = 1 and nstenergy = 1, please try that!!! In fact make everything 1 (nstxout,nstxtcout,...) Here is what worked for me with the same POPE file: 1. Do an energy minimization 2. run the make_hole mdrun: grompp -maxwarn 10000 -f grompp_md.mdp -c a.gro -p a.top -o a.tpr mdrun -nice 4 -hole -holep hole.mdp -s a.tpr -o a.trr -c b.gro -g output.mdrun -v -x a.xtc ############################# em.mdp ############################ title = energyMinimization cpp = /usr/bin/cpp integrator = steep nsteps = 500 emtol = 200 emstep = 0.000005 comm_mode = linear nstcomm = 1 comm_grps = System ns_type = grid pbc = xyz coulombtype = PME fourierspacing = 0.15 pme_order = 4 vdwtype = switch rvdw_switch = 0.9 rvdw = 1.0 rlist = 1.1 DispCorr = no Pcoupl = no tcoupl = no annealing = no gen_seed = 9896 constraints = hbonds constraint_algorithm= shake shake_tol = 0.0001 ############################# hole.mdp ############################ holetype = Grasp_ascii hfm = 10 supf = 10 molsurf_log = make_hole.log hr = 0 hx = 0 hy = 0 hz = 3.5 hp1 = 1 hp2 = 17680 s1 = 17681 s2 = 43934 hz1 = 1.0 hz2 = 6.0 sfm = 10.0 sofs = 0 molsurf_file = pagpsys_tot_e.surf debugsurf = no resforces = yes ############################ run.mdp ################################# title = seriousMD cpp = /usr/bin/cpp define = -DPOSRES integrator = md nsteps = 10000 tinit = 0 dt = 0.002 comm_mode = None nstcomm = 1 comm_grps = System nstxout = 10000 nstvout = 10000 nstfout = 10000 nstlog = 100 nstlist = 10 nstenergy = 10000 nstxtcout = 250 ns_type = grid pbc = xyz coulombtype = Cut-off ;fourierspacing = 0.15 ;pme_order = 4 vdwtype = switch rvdw_switch = 0.9 rvdw = 1.1 rlist = 1.1 rcoulomb = 1.1 DispCorr = no Pcoupl = Berendsen tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1. tcoupl = nose-hoover tc_grps = POPE SOL tau_t = 0.05 0.05 ref_t = 300. 300. annealing = no gen_vel = yes gen_temp = 300. gen_seed = 9896 constraints = hbonds constraint_algorithm= shake shake_tol = 0.0001 From chris.neale at utoronto.ca Tue Sep 5 02:19:48 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Mon, 4 Sep 2006 20:19:48 -0400 Subject: [gmx-users] RB-dihedral replacing 1-4 interactions Message-ID: <1157415588.44fcc2a407609@webmail.utoronto.ca> "Bond rotations in the carbon tails were modeled with Ryckaert-Bellemans dihedrals and the corresponding 1,4 interactions removed" (Lindahl and Edholm, Biophys J., 79, 426-433) When doing a parameter substitution in this way, exactly what 1,4 interactions should be removed? I am using the pope.itp file from Dr. Tieleman's website and my specific question is why, when the double bond is atom 24 to atom 25, does the [pairs] group contain 22-25 and 24-27, but there are no defined [pairs] for 21-24 or 25-28? The general structure around the double bond looks like this: 21 LP2 22 LP2 23 LP2 24 LH1 || double bond 25 LH1 26 LP2 27 LP2 28 LP2 Below I have extracted any reference to atoms 21 to 28 from pope.itp: [ atoms ] 21 LP2 1 POPE C21 7 0 14.0270 ; qtot: 22 LP2 1 POPE C22 8 0 14.0270 ; qtot: 23 LP2 1 POPE C23 9 0 14.0270 ; qtot: 24 LH1 1 POPE C24 10 0 13.0190 ; qtot: 25 LH1 1 POPE C25 11 0 13.0190 ; qtot: 26 LP2 1 POPE C26 12 0 14.0270 ; qtot: 27 LP2 1 POPE C27 13 0 14.0270 ; qtot: 28 LP2 1 POPE C28 14 0 14.0270 ; qtot: [ bonds ] 21 22 1 0.15300E+00 0.33470E+06 22 23 1 0.15300E+00 0.33470E+06 23 24 1 0.15300E+00 0.33470E+06 24 25 1 0.13900E+00 0.41840E+06 ; double bond 25 26 1 0.15300E+00 0.33470E+06 26 27 1 0.15300E+00 0.33470E+06 27 28 1 0.15300E+00 0.33470E+06 [ pairs ] 22 25 1 ; pair around double bond 24 27 1 ; pair around double bond [ angles ] 21 22 23 1 0.11100E+03 0.46020E+03 22 23 24 1 0.11100E+03 0.46020E+03 23 24 25 1 120.000 502.080 ; cis thingies 24 25 26 1 120.000 502.080 ; cis thingies 25 26 27 1 0.11100E+03 0.46020E+03 26 27 28 1 0.11100E+03 0.46020E+03 [dihedrals] 21 22 23 24 3 22 23 24 25 1 0.000 5.858 3 23 24 25 26 2 0.000 167.360 24 25 26 27 1 0.000 5.858 3 25 26 27 28 3 Thanks for any assistance, Chris Neale. From Steven.Kirk at hv.se Tue Sep 5 09:42:32 2006 From: Steven.Kirk at hv.se (Steven Kirk) Date: Tue, 05 Sep 2006 09:42:32 +0200 Subject: [gmx-users] Energy minimization problem with macromolecule and polarizable water model Message-ID: <44FD2A68.5080104@hv.se> Hello, I recently obtained (from DvS) the .itp file for the SSWM4-DP polarizable water molecule, and a corresponding set of water box coordinates. I use double precision executables in all of the calculations mentioned below. I ran an energy minimization on this box of water, then a 500ps run (0.001ps timestep) at 300K with Berendsen pressure and temperature coupling (pressure time constant set to 10 ps), PME, EnerPres dispersion corrections, rlist=rcoulomb=rvdv=0.9. The shell particle was left massless. Everything seemed to be OK in the run, total/kinetic/potential energies settled nicely with no extreme fluctuations, density ended up about 998kg/m^3, no major temperature or box volume fluctuations. So then I took the final water box and used genbox to solvate a charged macromolecule with my shiny new water model, then added Na+ ions with genion until charge balance was achieved. I disabled the defaults line in the sswm4-dp.itp file, using instead OPLS-AA defaults and force field parameters for everything that wasn't water. Seemingly, so far so good. The problem arose when I tried to energy minimise my solvated macromolecule. Using the mdp settings: cpp = /lib/cpp define = constraints = none integrator = steep nsteps = 2000 ; ; Energy minimizing stuff ; emtol = 100 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1.0 coulomb-type = pme rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no lincs_iter = 4 the minimiser ran for about 100 steps, then converged to machine precision. Unfortunately the max force was still very large (E+06, on a water hydrogen). Reducing emstep and changing to the l-bfgs minimiser (cg minimiser was disallowed because of presence of constraints, presumably from the water model) had very little effect on the max force. In desperation I even tried a 10ps full MD run at 10K to see if this would ease the mysterious force problem a little, but got LINCS errors on the very first step. I'm now wondering if the problem is due to (working backwards): a) Incompatible settings in my production system (solvated macromolecule) b) genbox somehow mangling my equilibrated water molecules c) Some mistake in my original equilibration of the box of polarizable water. The LINCS errors suggest a structural problem, but if that arose in step c), surely it would be visible as LINCS errors in the water box equilibration run? This makes genbox my prime suspect. I would be very grateful for anyone's opinions on where I have gone wrong, and what I can do to fix the problem. Many thanks in advance, Steve Kirk -- Dr. Steven R. Kirk Dept. of Technology, Mathematics & Computer Science (P)+46 520 223215 University West (F)+46 520 223299 P.O. Box 957 Trollhattan 461 29 SWEDEN http://taconet.webhop.org From samuel.flores at yale.edu Tue Sep 5 16:17:50 2006 From: samuel.flores at yale.edu (Samuel C Flores) Date: Tue, 5 Sep 2006 10:17:50 -0400 Subject: [gmx-users] REMD In-Reply-To: <44FD2A68.5080104@hv.se> Message-ID: <200609051417.k85EHmEQ007516@pantheon-po11.its.yale.edu> Hi Guys, Can anyone point me to a tutorial on using REMD in Gromacs? I can't seem to find anything on the web. There is a package called RPMDRUN, but I don't see a reason to use outside packages when Gromacs, I believe, can handle everything itself. Sam -----Original Message----- From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Steven Kirk Sent: Tuesday, September 05, 2006 3:43 AM To: gmx-users at gromacs.org Subject: [gmx-users] Energy minimization problem with macromolecule and polarizable water model Importance: High Hello, I recently obtained (from DvS) the .itp file for the SSWM4-DP polarizable water molecule, and a corresponding set of water box coordinates. I use double precision executables in all of the calculations mentioned below. I ran an energy minimization on this box of water, then a 500ps run (0.001ps timestep) at 300K with Berendsen pressure and temperature coupling (pressure time constant set to 10 ps), PME, EnerPres dispersion corrections, rlist=rcoulomb=rvdv=0.9. The shell particle was left massless. Everything seemed to be OK in the run, total/kinetic/potential energies settled nicely with no extreme fluctuations, density ended up about 998kg/m^3, no major temperature or box volume fluctuations. So then I took the final water box and used genbox to solvate a charged macromolecule with my shiny new water model, then added Na+ ions with genion until charge balance was achieved. I disabled the defaults line in the sswm4-dp.itp file, using instead OPLS-AA defaults and force field parameters for everything that wasn't water. Seemingly, so far so good. The problem arose when I tried to energy minimise my solvated macromolecule. Using the mdp settings: cpp = /lib/cpp define = constraints = none integrator = steep nsteps = 2000 ; ; Energy minimizing stuff ; emtol = 100 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1.0 coulomb-type = pme rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no lincs_iter = 4 the minimiser ran for about 100 steps, then converged to machine precision. Unfortunately the max force was still very large (E+06, on a water hydrogen). Reducing emstep and changing to the l-bfgs minimiser (cg minimiser was disallowed because of presence of constraints, presumably from the water model) had very little effect on the max force. In desperation I even tried a 10ps full MD run at 10K to see if this would ease the mysterious force problem a little, but got LINCS errors on the very first step. I'm now wondering if the problem is due to (working backwards): a) Incompatible settings in my production system (solvated macromolecule) b) genbox somehow mangling my equilibrated water molecules c) Some mistake in my original equilibration of the box of polarizable water. The LINCS errors suggest a structural problem, but if that arose in step c), surely it would be visible as LINCS errors in the water box equilibration run? This makes genbox my prime suspect. I would be very grateful for anyone's opinions on where I have gone wrong, and what I can do to fix the problem. Many thanks in advance, Steve Kirk -- Dr. Steven R. Kirk Dept. of Technology, Mathematics & Computer Science (P)+46 520 223215 University West (F)+46 520 223299 P.O. Box 957 Trollhattan 461 29 SWEDEN http://taconet.webhop.org _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php From mgoette at mpi-bpc.mpg.de Tue Sep 5 14:35:43 2006 From: mgoette at mpi-bpc.mpg.de (Maik Goette) Date: Tue, 05 Sep 2006 14:35:43 +0200 Subject: [gmx-users] Possible Bug GROMACS 3.3.1 - NMA Message-ID: <44FD6F1F.2090507@mpi-bpc.mpg.de> Hi I just observed very strange results with my system (around 700 atoms in vacuum), when doing normal mode analysis. The eigenvalues were all negative. I then took an old nma-system from Bert de Groot and did the nma with 3.3.1 on it and observed the same strange results. After that I tried 3.2.1 on that system and the results were quite similar to the ones Bert got with 3.1.4. My vacuum-system yields (more or less) correct (not nice) results on the first look. Is there something new to obey in 3.3.1 what isn't mentioned in the manual (3.11 NMA)? If not, I would think, there's a bug. Any suggestions? Regards -- Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ From spoel at xray.bmc.uu.se Tue Sep 5 16:38:02 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Tue, 05 Sep 2006 16:38:02 +0200 Subject: [gmx-users] Possible Bug GROMACS 3.3.1 - NMA In-Reply-To: <44FD6F1F.2090507@mpi-bpc.mpg.de> References: <44FD6F1F.2090507@mpi-bpc.mpg.de> Message-ID: <44FD8BCA.1080604@xray.bmc.uu.se> Maik Goette wrote: > Hi > > I just observed very strange results with my system (around 700 atoms in > vacuum), when doing normal mode analysis. The eigenvalues were all > negative. > I then took an old nma-system from Bert de Groot and did the nma with > 3.3.1 on it and observed the same strange results. After that I tried > 3.2.1 on that system and the results were quite similar to the ones Bert > got with 3.1.4. > My vacuum-system yields (more or less) correct (not nice) results on the > first look. > > Is there something new to obey in 3.3.1 what isn't mentioned in the > manual (3.11 NMA)? > If not, I would think, there's a bug. > Any suggestions? > > Regards > Are you using cut-offs? In that case gromacs uses a different algorithm now, which might cause the problem. Anyway if you have a reproducible problem please report a bugzilla and upload the necessary files. -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From una.bjarnadottir at ucd.ie Tue Sep 5 18:27:39 2006 From: una.bjarnadottir at ucd.ie (Una Bjarnadottir) Date: Tue, 05 Sep 2006 17:27:39 +0100 Subject: [gmx-users] missing atom in .rpb: fatal error in pdb2gmx In-Reply-To: <20060309161528.B7F1B24D38@xray.bmc.uu.se> References: <20060309161528.B7F1B24D38@xray.bmc.uu.se> Message-ID: <44FDA57B.40308@ucd.ie> Dear Users, When running pdb2gmx I get this error: Program pdb2gmx, VERSION 3.3.1 Source code file: add_par.c, line: 221 Fatal error: Atom NZ1 not found in rtp database in residue LYSH, it looks a bit like NZ Dr. David van der Spoel already suggested to rename the atom in the pdb file which I did and than the same and than this error occured: Program pdb2gmx, VERSION 3.3.1 Source code file: pdb2gmx.c, line: 393 Fatal error: Atom NZ1 in residue LYSH 2 not found in rtp entry with 13 atoms while sorting atoms I changed the the NZ atoms in the .rtp file to NZ1 and than this came: Program pdb2gmx, VERSION 3.3.1 Source code file: add_par.c, line: 221 Fatal error: Atom NZ2 not found in rtp database in residue LYSH, it looks a bit like NZ1. I don't understand the problem because in the beginning there was no atom called NZ1 in the .pdb file or the .rdb file and than why is pdb2gmx complaining about this atom in the first place? Thanks in advance, replys are highly appreciated. Una Bjarnadottir From melicher at cray.dbp.fmph.uniba.sk Tue Sep 5 20:03:53 2006 From: melicher at cray.dbp.fmph.uniba.sk (Milan Melichercik) Date: Tue, 5 Sep 2006 20:03:53 +0200 Subject: [gmx-users] radial densities Message-ID: <200609052003.53761.melicher@cray.dbp.fmph.uniba.sk> Hi guys, maybe I ask stupid question and I missed something, but I want to compute radial densities (perpendicular to an axis of a alpha helix peptide), but I couldn't find suitable program to do this job. Thanks a lot for help Milan From alokjain at iitk.ac.in Tue Sep 5 20:14:45 2006 From: alokjain at iitk.ac.in (Alok) Date: Tue, 5 Sep 2006 23:44:45 +0530 Subject: [gmx-users] mdrun_hole problem again ..SOLVED..THANKS..... References: <1157411103.44fcb11f690ef@webmail.utoronto.ca> Message-ID: <000801c6d117$2aa53180$65741aac@alok> Thanks a lot to all of you, especialy Florian and Chris. My problem has been solved. Best regards, Alok ----- Original Message ----- From: To: Sent: Tuesday, September 05, 2006 4:35 AM Subject: Re: [gmx-users] mdrun_hole problem again >- you didn't do an energy minimization > - you used hz1 0 and I used hz1 1.0 > - you didn't include make hole options hr,hx,hy > > *** Somebody already suggested nstlog = 1 and nstenergy = 1, please try > that!!! > In fact make everything 1 (nstxout,nstxtcout,...) > > Here is what worked for me with the same POPE file: > > 1. Do an energy minimization > > 2. run the make_hole mdrun: > > grompp -maxwarn 10000 -f grompp_md.mdp -c a.gro -p a.top -o a.tpr > > mdrun -nice 4 -hole -holep hole.mdp -s a.tpr -o a.trr -c b.gro -g > output.mdrun > -v -x a.xtc > > ############################# em.mdp ############################ > > title = energyMinimization > cpp = /usr/bin/cpp > integrator = steep > nsteps = 500 > emtol = 200 > emstep = 0.000005 > comm_mode = linear > nstcomm = 1 > comm_grps = System > ns_type = grid > pbc = xyz > coulombtype = PME > fourierspacing = 0.15 > pme_order = 4 > vdwtype = switch > rvdw_switch = 0.9 > rvdw = 1.0 > rlist = 1.1 > DispCorr = no > Pcoupl = no > tcoupl = no > annealing = no > gen_seed = 9896 > constraints = hbonds > constraint_algorithm= shake > shake_tol = 0.0001 > > > ############################# hole.mdp ############################ > > holetype = Grasp_ascii > hfm = 10 > supf = 10 > molsurf_log = make_hole.log > hr = 0 > hx = 0 > hy = 0 > hz = 3.5 > hp1 = 1 > hp2 = 17680 > s1 = 17681 > s2 = 43934 > hz1 = 1.0 > hz2 = 6.0 > sfm = 10.0 > sofs = 0 > molsurf_file = pagpsys_tot_e.surf > debugsurf = no > resforces = yes > > ############################ run.mdp ################################# > title = seriousMD > cpp = /usr/bin/cpp > define = -DPOSRES > integrator = md > nsteps = 10000 > tinit = 0 > dt = 0.002 > comm_mode = None > nstcomm = 1 > comm_grps = System > nstxout = 10000 > nstvout = 10000 > nstfout = 10000 > nstlog = 100 > nstlist = 10 > nstenergy = 10000 > nstxtcout = 250 > ns_type = grid > pbc = xyz > coulombtype = Cut-off > ;fourierspacing = 0.15 > ;pme_order = 4 > vdwtype = switch > rvdw_switch = 0.9 > rvdw = 1.1 > rlist = 1.1 > rcoulomb = 1.1 > DispCorr = no > Pcoupl = Berendsen > tau_p = 0.5 > compressibility = 4.5e-5 > ref_p = 1. > tcoupl = nose-hoover > tc_grps = POPE SOL > tau_t = 0.05 0.05 > ref_t = 300. 300. > annealing = no > gen_vel = yes > gen_temp = 300. > gen_seed = 9896 > constraints = hbonds > constraint_algorithm= shake > shake_tol = 0.0001 > > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > From alokjain at iitk.ac.in Tue Sep 5 20:18:55 2006 From: alokjain at iitk.ac.in (Alok) Date: Tue, 5 Sep 2006 23:48:55 +0530 Subject: [gmx-users] OPLS + ffgmx References: <200609052003.53761.melicher@cray.dbp.fmph.uniba.sk> Message-ID: <001201c6d117$bf8debc0$65741aac@alok> Hi all, I am trying to do a membrane protein simulation. I want to use OPLS - AA force field for protein and ffgmx (modified ffgmx force filed with lipid parameters from user contribution section ) force field for POPE lipids. Is it is possible and advisable to use two different force fields for protein and lipids? Or else, Is there any all atom force field availble for lipid molecules which I can use? I read a mail from Chris regarding the same, http://www.gromacs.org/pipermail/gmx-users/2006-May/021416.html But procedure is not very clear to me. Could you please explain me more explicitly. Thanks a lot, Alok From chris.neale at utoronto.ca Tue Sep 5 23:34:08 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Tue, 5 Sep 2006 17:34:08 -0400 Subject: [gmx-users] OPLS + ffgmx Message-ID: <1157492048.44fded50b4b92@webmail.utoronto.ca> I posted the procedure and not the modified files mostly because this is my modification of somebody else's files. Without permission, it is not reasonable for me to redistribute them. In order to both help you and still treat the originals with due respect, I have attached snippets that will help you to make your own modifications. It should not take very long for you to copy the procedure. Regarding the advisability of combining the Berger lipids and the OPLS-AA force field... Read this: Tieleman et. al. J. Phys.:Condens. Matter 18 (2006) S1221-34 As for my own interpretation (of course that depends on your system and what question you are trying to answer): If you are focusing mostly on the protein and just want a pretty good lipid, then yes, I personally think it's a good combo. If you are focusing on the lipid behaviour around the protein then you run into more difficulty, but then again there really aren't any good fields for that as far as I know. I am not sure how good the Berger lipid / gromos field combination represents that either. Follow the procedure here: http://www.gromacs.org/pipermail/gmx-users/2006-May/021416.html When it says: 1. Added [atomtypes] from lipid.itp to ffoplsaanb.itp -- after changing c6/c12 to sigma/epsilon. Also added atomtype H from olsa_369 to match H expected by pope.itp - sigma = (c12/c6)^1/6 - epsilon = c6/(4*sigma^6) Do this: a) Using some script of your own or MS Excel convert the c6 and c12 values to sigma and epsilon values as per the noted equations. b) Take the [atomtypes] section from lipid.itp to the [atomtypes] section of ffoplsaanb.itp. Since ffoplsaanb.itp has only one section, and it is [atomtypes], just paste it to the bottom. When it says: 2. Added [pairtypes] from lipid.itp to ffoplsaanb.itp -- after changing c6/c12 to sigma/epsilon. (gives effective fudgeLJ of 0.125). Also changed all reference to OW to opls_116 (opls spc water oxygen) and simply removed any with reference to HW as it will be zero regardless. Do this: c) Make the same c6/c12 -> sigma/epsilon changes and paste the section ([pairtypes] identifier and all) to the bottom of the new ffoplsaanb.itp file. When it says: 3. Added [dihedraltypes] from lipid.itp to ffoplsaabon.itp. - Prior to running ensure that the non-RB dihedral does not exist for these groups. Do this: d) paste the following segment to the bottom of ffoplsaabon.itp: ; Added by Chris Neale April 16 2006 based on ; lipid.inp from http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies ; Based on Berger et al, Biophys. J. (1997) 72, pp. 2002-2013. ; Copy and paste from lipid.inp ;[ bondtypes ] ;[ constrainttypes ] ;[ angletypes ] [ dihedraltypes ] ; i j func coefficients LP2 LP2 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495 etc... e) Then make your topology file according to what was already laid out in section 4 of the previous post. ############################# The relevant addition from my ffoplsaanb.itp file ; Added by Chris Neale April 16 2006 based on ; lipid.inp from http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies ; Based on Berger et al, Biophys. J. (1997) 72, pp. 2002-2013. ; Copy and paste from lipid.inp then duplicate first column and add zero in 3rd column ; Then comment out initial version (with C6 and C12) and replace with sigma and epsilon ; NOTE considered the use of epsilon LOS 0.711 (Berger/OPLS?) not 0.879 (Tieleman) ; HOWEVER, dihedrals etc are set up for 0.879 therefore use that one ; Also added name = H from opls_369 to match H expected by pope.itp ; Also changed 3rd column from all zeros to all ones LO LO 1 15.9994 0.000 A 2.96000e-01 8.87864e-01 ;carbonyl O, OPLS LOM LOM 1 15.9994 0.000 A 2.96000e-01 8.87864e-01 ;carbonyl O, OPLS LNL LNL 1 14.0067 0.000 A 3.25000e-01 7.11280e-01 ;Nitrogen, OPLS etc... ; Added by Chris Neale May 1 2006 based on ; lipid.inp from http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies ; Based on Berger et al, Biophys. J. (1997) 72, pp. 2002-2013. ; Copy and paste from lipid.inp into excel then convert c6 and c12 to sigma and epsilon ; sigma=power(c12/c6,1/6) and epsilon=c6/(4*power(sigma,6)) ; NOTE direct conversion therefore using LOS epsilon 0.879 as Tieleman ; Removed all SPC hydrogen as they will be calculated as zero anyway ; This was required so as to give LJ14 values involving lipid-lipid a fudgeLJ value of 0.125 [ pairtypes ] ; i j funct sigma epsilon LO LO 1 2.96E-01 1.10E-01 LO LOM 1 2.96E-01 1.10E-01 LO opls_116 1 3.06E-01 9.47E-02 LO LNL 1 3.10E-01 9.88E-02 LO LC 1 3.33E-01 7.76E-02 etc... From mark.abraham at anu.edu.au Wed Sep 6 04:17:51 2006 From: mark.abraham at anu.edu.au (Mark Abraham) Date: Wed, 6 Sep 2006 12:17:51 +1000 (EST) Subject: [gmx-users] OPLS + ffgmx In-Reply-To: <001201c6d117$bf8debc0$65741aac@alok> References: <200609052003.53761.melicher@cray.dbp.fmph.uniba.sk> <001201c6d117$bf8debc0$65741aac@alok> Message-ID: <37402.150.203.145.27.1157509071.squirrel@sqmail.anu.edu.au> > Hi all, > > I am trying to do a membrane protein simulation. I want to use OPLS - AA > force field for protein and ffgmx (modified ffgmx force filed with lipid > parameters from user contribution section ) force field for POPE lipids. > > Is it is possible and advisable to use two different force fields for > protein and lipids? In general, this way madness lies. Force fields are mathematical constructs that are optimized to approximately reproduce some experimental properties *in cooperation with itself*. There is no reason to expect that force field parameters for "bond strength" have any great correlation with an experimentally determined bond strength, and thus to have no correlation with a "bond strength" from another force field. Accordingly there's no reason to expect that a mixture of parts of different force fields will work well together. It's somewhat like taking half of a soccer team and half of a gridiron team and expecting them to be able to play rugby together. > Or else, Is there any all atom force field availble for lipid molecules > which I can use? CHARMM parameter sets optimized for combined protein & lipid calculations exist. Simplest would then be to use CHARMM or NAMD. If you want to use GROMACS, you can get such a force field, use my scripts available here http://www.gromacs.org/contributed_by_users/task,doc_details/gid,59/ to convert them to gromacs format, obtain some .rtp files elsewhere, test carefully, and simulate to your heart's content. Mark From chris.neale at utoronto.ca Wed Sep 6 09:53:06 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Wed, 6 Sep 2006 03:53:06 -0400 Subject: [gmx-users] radial densities Message-ID: <1157529186.44fe7e6235bd3@webmail.utoronto.ca> Can't think of a current program that does this. One option is to: 1. Use g_sdf from here: http://www.gromacs.org/pipermail/gmx-developers/2006-August/001786.html 1b. With the bug fix from here: http://www.gromacs.org/pipermail/gmx-developers/2006-August/001791.html BUG: line 216 of 298 should have divided Y and Z by "bohr", not just X as was previously posted. The correct line is: fprintf(flp,"%5d%12.6f%12.6f%12.6f\n",nidxp,(MINBIN[XX]+(minx+iIGNOREOUTER) *rBINWIDTH)*10./bohr,(MINBIN[YY]+(miny+iIGNOREOUTER)*rBINWIDTH)*10./bohr, (MINBIN[ZZ]+(minz+iIGNOREOUTER)*rBINWIDTH)*10./bohr); 1c. With the fixed order of alignment prior to running g_sdf from here: http://www.gromacs.org/pipermail/gmx-users/2006-August/023549.html trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans This will give you the spatial distribution function... not quite what you want. However, you could easily write a bash script that converted this spatial distribution function into an all-helix radial distribution function (if I am correct that you intend to derive a single plot with radial distance on the x axis and a density-given-x over the y axis). From mgoette at mpi-bpc.mpg.de Wed Sep 6 10:25:01 2006 From: mgoette at mpi-bpc.mpg.de (Maik Goette) Date: Wed, 06 Sep 2006 10:25:01 +0200 Subject: [gmx-users] Possible Bug GROMACS 3.3.1 - NMA In-Reply-To: <44FD8BCA.1080604@xray.bmc.uu.se> References: <44FD6F1F.2090507@mpi-bpc.mpg.de> <44FD8BCA.1080604@xray.bmc.uu.se> Message-ID: <44FE85DD.9090006@mpi-bpc.mpg.de> Yes, I'm using Cut-off. And the Error is reproducable. I'll post the bug report. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ David van der Spoel wrote: > Maik Goette wrote: > >> Hi >> >> I just observed very strange results with my system (around 700 atoms >> in vacuum), when doing normal mode analysis. The eigenvalues were all >> negative. >> I then took an old nma-system from Bert de Groot and did the nma with >> 3.3.1 on it and observed the same strange results. After that I tried >> 3.2.1 on that system and the results were quite similar to the ones >> Bert got with 3.1.4. >> My vacuum-system yields (more or less) correct (not nice) results on >> the first look. >> >> Is there something new to obey in 3.3.1 what isn't mentioned in the >> manual (3.11 NMA)? >> If not, I would think, there's a bug. >> Any suggestions? >> >> Regards >> > Are you using cut-offs? In that case gromacs uses a different algorithm > now, which might cause the problem. Anyway if you have a reproducible > problem please report a bugzilla and upload the necessary files. > From kameda-tomoshi at aist.go.jp Wed Sep 6 12:33:15 2006 From: kameda-tomoshi at aist.go.jp (Tomoshi Kameda) Date: Wed, 06 Sep 2006 19:33:15 +0900 Subject: [gmx-users] trjconv for hexa-meric protein Message-ID: <20060906190349.B5DD.KAMEDA-TOMOSHI@aist.go.jp> Hi I simulate a hexa-meric protein (443*6=2658 residues with about 90000 water) Especially, I'm interested in water behavior around the protein. The 1ns simulation is finished normally, but trjconv produces abnormal structure. For example, the protein go outside my waterbox, water molecules are diverse abnormally...etc. I try various options: trjconv -s full.tpr -f full.trr -o full.xtc -pbc nojump trjconv -s full.tpr -f full.trr -o full.xtc -pbc cluster trjconv -s full.tpr -f full.trr -o full.xtc -fit rot (select 1(thus protein) for fitting group) And, I watch full.xtc using VMD, but they are strange in all cases. For your information, I use cubic periodic boundary condition. Please suggest me. Greetings, Tomoshi From carsten.baldauf at biotec.tu-dresden.de Wed Sep 6 13:43:00 2006 From: carsten.baldauf at biotec.tu-dresden.de (Carsten Baldauf) Date: Wed, 06 Sep 2006 13:43:00 +0200 Subject: [gmx-users] change number of processors after tpbconv Message-ID: <44FEB444.4030107@biotec.tu-dresden.de> hi all// is it possible to change the number of processors (mpi) when i try to continue a crashed/stopped run with tpbconv? cheers// carsten From spoel at xray.bmc.uu.se Wed Sep 6 13:45:46 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Wed, 06 Sep 2006 13:45:46 +0200 Subject: [gmx-users] change number of processors after tpbconv In-Reply-To: <44FEB444.4030107@biotec.tu-dresden.de> References: <44FEB444.4030107@biotec.tu-dresden.de> Message-ID: <44FEB4EA.1010307@xray.bmc.uu.se> Carsten Baldauf wrote: > hi all// > is it possible to change the number of processors (mpi) when i try to > continue a crashed/stopped run with tpbconv? > cheers// > carsten > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php No, you have to use grompp -t -e -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From alokjain at iitk.ac.in Wed Sep 6 21:48:47 2006 From: alokjain at iitk.ac.in (Alok) Date: Thu, 7 Sep 2006 01:18:47 +0530 Subject: [gmx-users] OPLS + ffgmx References: <200609052003.53761.melicher@cray.dbp.fmph.uniba.sk><001201c6d117$bf8debc0$65741aac@alok> <37402.150.203.145.27.1157509071.squirrel@sqmail.anu.edu.au> Message-ID: <002e01c6d1ed$77ac4230$65741aac@alok> Hi Mark and Chris, Thanks a lot to both of you for going through my query, for suggesting the positive and negative points of this procedure. I will think and then decide how to go about it. I am really thankful to Chris for the detailed suggestion regarding the procedure. I will come back to you later as I go about it. Thanking you all again, Regards, Alok. ----- Original Message ----- From: "Mark Abraham" To: "Discussion list for GROMACS users" Sent: Wednesday, September 06, 2006 7:47 AM Subject: Re: [gmx-users] OPLS + ffgmx > Hi all, > > I am trying to do a membrane protein simulation. I want to use OPLS - AA > force field for protein and ffgmx (modified ffgmx force filed with lipid > parameters from user contribution section ) force field for POPE lipids. > > Is it is possible and advisable to use two different force fields for > protein and lipids? In general, this way madness lies. Force fields are mathematical constructs that are optimized to approximately reproduce some experimental properties *in cooperation with itself*. There is no reason to expect that force field parameters for "bond strength" have any great correlation with an experimentally determined bond strength, and thus to have no correlation with a "bond strength" from another force field. Accordingly there's no reason to expect that a mixture of parts of different force fields will work well together. It's somewhat like taking half of a soccer team and half of a gridiron team and expecting them to be able to play rugby together. > Or else, Is there any all atom force field availble for lipid molecules > which I can use? CHARMM parameter sets optimized for combined protein & lipid calculations exist. Simplest would then be to use CHARMM or NAMD. If you want to use GROMACS, you can get such a force field, use my scripts available here http://www.gromacs.org/contributed_by_users/task,doc_details/gid,59/ to convert them to gromacs format, obtain some .rtp files elsewhere, test carefully, and simulate to your heart's content. Mark _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php From carsten.baldauf at biotec.tu-dresden.de Thu Sep 7 00:26:27 2006 From: carsten.baldauf at biotec.tu-dresden.de (Carsten Baldauf) Date: Thu, 07 Sep 2006 00:26:27 +0200 Subject: [gmx-users] change number of processors after tpbconv In-Reply-To: <44FEB4EA.1010307@xray.bmc.uu.se> References: <44FEB444.4030107@biotec.tu-dresden.de> <44FEB4EA.1010307@xray.bmc.uu.se> Message-ID: <44FF4B13.2020909@biotec.tu-dresden.de> thank you// David van der Spoel wrote: > Carsten Baldauf wrote: >> hi all// >> is it possible to change the number of processors (mpi) when i try to >> continue a crashed/stopped run with tpbconv? >> cheers// >> carsten >> _______________________________________________ >> gmx-users mailing list gmx-users at gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-request at gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > No, you have to use grompp -t -e > From dai at ripp-sinopec.com Thu Sep 7 04:14:25 2006 From: dai at ripp-sinopec.com (=?GBK?B?tPrV8dPu?=) Date: Thu, 7 Sep 2006 10:14:25 +0800 (CST) Subject: [gmx-users] about gromacs Message-ID: <25024838.1157595266784.JavaMail.root@oaserver> Hello, everyone: Would you please tell me that whether Gromacs can be used to do Molecular Dynamics studies for Polymer like PVC or PET? Thanks a lot. dai0601 2006-09-07 From zgxjlx at gmail.com Thu Sep 7 04:57:09 2006 From: zgxjlx at gmail.com (liu xin) Date: Thu, 7 Sep 2006 10:57:09 +0800 Subject: [gmx-users] Simulation problem with extended membrane system! In-Reply-To: <1157410096.44fcad30a63f9@webmail.utoronto.ca> References: <1157410096.44fcad30a63f9@webmail.utoronto.ca> Message-ID: Hi Chris Thank you for your suggestions! These days I also tried anisotropic and semiisotropic for my simulation, but I still got the same result, so I wonder maybe there's something wrong with my initial structure, but it will take time to check it out. I'm trying to use the method you suggested, I searched the list, find there is some scripts offered by other users, but I'm new to Linux and gromacs, I've got no idea which one to use and how to use it. So would you please send me a sample? Thank you very much for your help Xin Liu On 9/5/06, chris.neale at utoronto.ca wrote: > > It is unclear why your second method works for you. However, given that it > does, > just use genbox -cs spc216.gro -cp 183_system_that_worked.gro -box 9.2 9.2 > 8.3 > and then use your own script to remove any spc waters that were put inside > the > membrane and modify the nubers in your topology file accordingly. > > I imagine that your first attempt didn't work since an entire dppc > molecule is > removed upon a single collision and this will lead to "holes" in your > membrane > that will quickly fill with water. Of course this should also have > happened in > your second attempt... I am not sure what was different there. > > You need semiisotropic pressure coupling and you need to stop every once > and a > while and remove any water molecules that are inside the membrane. Note > that > isotropic Pcoupling in a membrane system (as you have been doing) has the > potential to provide a surface tension (or the opposite) that you have not > been > intentionally including and so you can expect your membrane to behave > differently. > > Chris. > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -------------- next part -------------- An HTML attachment was scrubbed... URL: From spoel at xray.bmc.uu.se Thu Sep 7 08:59:56 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Thu, 07 Sep 2006 08:59:56 +0200 Subject: [gmx-users] about gromacs In-Reply-To: <25024838.1157595266784.JavaMail.root@oaserver> References: <25024838.1157595266784.JavaMail.root@oaserver> Message-ID: <44FFC36C.5000500@xray.bmc.uu.se> ??? wrote: > Hello, everyone: > > Would you please tell me that whether Gromacs can be used to do Molecular Dynamics studies for Polymer like PVC or PET? Thanks a lot. > yes if you provide the input files. gromacs does not have many tools to deal with preparing input files for such systems, but have a look at genbox. > dai0601 > > 2006-09-07 > > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From anwar at cdfd.org.in Thu Sep 7 16:12:56 2006 From: anwar at cdfd.org.in (anwar at cdfd.org.in) Date: Thu, 7 Sep 2006 07:12:56 -0700 (PDT) Subject: [gmx-users] invacuo minimization Message-ID: <3910409.1157608829468.JavaMail.nobody@sunserver> Dear gmx users, When I am minimizing a trimer protein in vacuum by SD as well as CG methods, one of the monomer gets apart from the rest of the protein and places itself away from the other two monomers, which are intact. No periodic box is assigned. But when I am running editconf and assigning a box, then the structures are intact. What is the reason for the above behaviour? I am pasting the em.mdp below: cpp = /lib/cpp define = -DFLEX_SPC constraints = none ;integrator = CG integrator = steep nsteps = 1000 ; ; Energy minimizing stuff ; emtol = 100 ;for SD emstep = 0.1 ;for CG ;emstep = 0.001 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no Anwar ---------------------- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 anwar.m1 at gmail.com ----------------------- - From spoel at xray.bmc.uu.se Thu Sep 7 10:44:52 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Thu, 07 Sep 2006 10:44:52 +0200 Subject: [gmx-users] invacuo minimization In-Reply-To: <3910409.1157608829468.JavaMail.nobody@sunserver> References: <3910409.1157608829468.JavaMail.nobody@sunserver> Message-ID: <44FFDC04.4030707@xray.bmc.uu.se> anwar at cdfd.org.in wrote: > Dear gmx users, > When I am minimizing a trimer protein in vacuum by SD as well as CG methods, > one of the monomer gets apart from the rest of the protein and places itself > away from the other two monomers, which are intact. No periodic box is > assigned. But when I am running editconf and assigning a box, then the > structures are intact. What is the reason for the above behaviour? > I am pasting the em.mdp below: chekc your mdout.dmp, the default pbc = xyz > > cpp = /lib/cpp > define = -DFLEX_SPC > constraints = none > ;integrator = CG > integrator = steep > nsteps = 1000 > ; > ; Energy minimizing stuff > ; > emtol = 100 > ;for SD > emstep = 0.1 > ;for CG > ;emstep = 0.001 > > nstcomm = 1 > ns_type = grid > rlist = 1 > rcoulomb = 1.0 > rvdw = 1.0 > Tcoupl = no > Pcoupl = no > gen_vel = no > > > Anwar > > ---------------------- > Mohd Anwaruddin > Project Assistant > C/o DR.H.A.Nagarajaram > Lab of Computational Biology and Bioinformatics > Center for DNA Fingerprinting and Diagnostics(CDFD) > Nacharam > Hyderabad-500 076 > INDIA. > Tel: +91-8413-235467,68,69,70 ext 2019 > anwar.m1 at gmail.com > ----------------------- > > > > - > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From Mikko.Hellgren at ki.se Thu Sep 7 11:31:39 2006 From: Mikko.Hellgren at ki.se (Mikko Hellgren) Date: Thu, 07 Sep 2006 11:31:39 +0200 Subject: [gmx-users] LIE energy calculation! Message-ID: Hi Dear users, I have started to do calculations of the binding between a protein and different ligands. I have read articles on the LIE method and one tutorial. But still I have some quite general questions. I am using Cut-off and NVT ensamble. 1. When I run my ligands in a water solution without the protein, should I add counterions (Cl and Na) at physiological concentrations (about 10mM to 100mM) or make the system neutral with one or two ions or can I ignore any ions the simulation. 2. Should I put any restraints on the ligand in the simulation without the protein? 3. When I run my ligand bound to the protein. Should I put restraints (c-alpha, all atoms) on both protein and ligand or only protein or ligand or neither of them? My initial thought would be to put restraint on c-alpha of the protein and let the rest of the system be "free". Mikko ____________________________________________________ One cannot avoid making mistakes if one tries to produce a set of words, or of mathematical formulae, to describe nature. Nature is more complicated than language or mathematics. Nevertheless, one must do one's best to produce a set of symbols which are not to discordant with the facts. J.B.S. Haldane, preface to "What is Life?", Lindsay Drummond, 1949 -------------- next part -------------- A non-text attachment was scrubbed... Name: mikhel.vcf Type: text/x-vcard Size: 343 bytes Desc: Card for Mikko Hellgren URL: From anwar at cdfd.org.in Thu Sep 7 18:51:57 2006 From: anwar at cdfd.org.in (anwar at cdfd.org.in) Date: Thu, 7 Sep 2006 09:51:57 -0700 (PDT) Subject: [gmx-users] Re: invacuo minimization Message-ID: <32348103.1157618369892.JavaMail.nobody@sunserver> Hi David, I have checked the mdout.mdp and as you said it has pbc = xyz. What do I do now. I havent run editconf, but why it is taking pbc conditions? How do I remove these?? thanks Anwar ---------------------- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 anwar.m1 at gmail.com ----------------------- ---------REPLY TO------------- Date:Thu Sep 07 18:00:08 GMT+08:00 2006 FROM: gmx-users-request at gromacs.org To: gmx-users at gromacs.org Subject: gmx-users Digest, Vol 29, Issue 14 Send gmx-users mailing list submissions to gmx-users at gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-request at gromacs.org You can reach the person managing the list at gmx-users-owner at gromacs.org When replying, please edit your Subject line so it is more specific than "Re: Contents of gmx-users digest..." Today's Topics: 1. Re: invacuo minimization (David van der Spoel) 2. LIE energy calculation! (Mikko Hellgren) ---------------------------------------------------------------------- Message: 1 Date: Thu, 07 Sep 2006 10:44:52 +0200 From: David van der Spoel Subject: Re: [gmx-users] invacuo minimization To: Discussion list for GROMACS users Message-ID: <44FFDC04.4030707 at xray.bmc.uu.se> Content-Type: text/plain; charset=ISO-8859-1; format=flowed anwar at cdfd.org.in wrote: > Dear gmx users, > When I am minimizing a trimer protein in vacuum by SD as well as CG methods, > one of the monomer gets apart from the rest of the protein and places itself > away from the other two monomers, which are intact. No periodic box is > assigned. But when I am running editconf and assigning a box, then the > structures are intact. What is the reason for the above behaviour? > I am pasting the em.mdp below: chekc your mdout.dmp, the default pbc = xyz > > cpp = /lib/cpp > define = -DFLEX_SPC > constraints = none > ;integrator = CG > integrator = steep > nsteps = 1000 > ; > ; Energy minimizing stuff > ; > emtol = 100 > ;for SD > emstep = 0.1 > ;for CG > ;emstep = 0.001 > > nstcomm = 1 > ns_type = grid > rlist = 1 > rcoulomb = 1.0 > rvdw = 1.0 > Tcoupl = no > Pcoupl = no > gen_vel = no > > > Anwar > > ---------------------- > Mohd Anwaruddin > Project Assistant > C/o DR.H.A.Nagarajaram > Lab of Computational Biology and Bioinformatics > Center for DNA Fingerprinting and Diagnostics(CDFD) > Nacharam > Hyderabad-500 076 > INDIA. > Tel: +91-8413-235467,68,69,70 ext 2019 > anwar.m1 at gmail.com > ----------------------- > > > > - > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ------------------------------ Message: 2 Date: Thu, 07 Sep 2006 11:31:39 +0200 From: Mikko Hellgren Subject: [gmx-users] LIE energy calculation! To: "gmx-users at gromacs.org" Message-ID: Content-Type: text/plain; charset="us-ascii" Hi Dear users, I have started to do calculations of the binding between a protein and different ligands. I have read articles on the LIE method and one tutorial. But still I have some quite general questions. I am using Cut-off and NVT ensamble. 1. When I run my ligands in a water solution without the protein, should I add counterions (Cl and Na) at physiological concentrations (about 10mM to 100mM) or make the system neutral with one or two ions or can I ignore any ions the simulation. 2. Should I put any restraints on the ligand in the simulation without the protein? 3. When I run my ligand bound to the protein. Should I put restraints (c-alpha, all atoms) on both protein and ligand or only protein or ligand or neither of them? My initial thought would be to put restraint on c-alpha of the protein and let the rest of the system be "free". Mikko ____________________________________________________ One cannot avoid making mistakes if one tries to produce a set of words, or of mathematical formulae, to describe nature. Nature is more complicated than language or mathematics. Nevertheless, one must do one's best to produce a set of symbols which are not to discordant with the facts. J.B.S. Haldane, preface to "What is Life?", Lindsay Drummond, 1949 -------------- next part -------------- A non-text attachment was scrubbed... Name: mikhel.vcf Type: text/x-vcard Size: 343 bytes Desc: Card for Mikko Hellgren Url : http://www.gromacs.org/pipermail/gmx-users/attachments/20060907/9db7c71d/mikhel-0001.vcf ------------------------------ _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users End of gmx-users Digest, Vol 29, Issue 14 ***************************************** - From spoel at xray.bmc.uu.se Thu Sep 7 13:22:47 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Thu, 07 Sep 2006 13:22:47 +0200 Subject: [gmx-users] Re: invacuo minimization In-Reply-To: <32348103.1157618369892.JavaMail.nobody@sunserver> References: <32348103.1157618369892.JavaMail.nobody@sunserver> Message-ID: <45000107.7020903@xray.bmc.uu.se> anwar at cdfd.org.in wrote: > Hi David, > I have checked the mdout.mdp and as you said it has pbc = xyz. What do > I do now. I havent run editconf, but why it is taking pbc conditions? How > do I remove these?? pbc=no > thanks > Anwar > > ---------------------- > Mohd Anwaruddin > Project Assistant > C/o DR.H.A.Nagarajaram > Lab of Computational Biology and Bioinformatics > Center for DNA Fingerprinting and Diagnostics(CDFD) > Nacharam > Hyderabad-500 076 > INDIA. > Tel: +91-8413-235467,68,69,70 ext 2019 > anwar.m1 at gmail.com > ----------------------- > > > > ---------REPLY TO------------- > Date:Thu Sep 07 18:00:08 GMT+08:00 2006 > FROM: gmx-users-request at gromacs.org > To: gmx-users at gromacs.org > Subject: gmx-users Digest, Vol 29, Issue 14 > Send gmx-users mailing list submissions to > gmx-users at gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-request at gromacs.org > > You can reach the person managing the list at > gmx-users-owner at gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Re: invacuo minimization (David van der Spoel) > 2. LIE energy calculation! (Mikko Hellgren) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 07 Sep 2006 10:44:52 +0200 > From: David van der Spoel > Subject: Re: [gmx-users] invacuo minimization > To: Discussion list for GROMACS users > Message-ID: <44FFDC04.4030707 at xray.bmc.uu.se> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > anwar at cdfd.org.in wrote: >> Dear gmx users, >> When I am minimizing a trimer protein in vacuum by SD as well as CG methods, >> one of the monomer gets apart from the rest of the protein and places > itself >> away from the other two monomers, which are intact. No periodic box is >> assigned. But when I am running editconf and assigning a box, then the >> structures are intact. What is the reason for the above behaviour? >> I am pasting the em.mdp below: > > chekc your mdout.dmp, the default pbc = xyz > >> cpp = /lib/cpp >> define = -DFLEX_SPC >> constraints = none >> ;integrator = CG >> integrator = steep >> nsteps = 1000 >> ; >> ; Energy minimizing stuff >> ; >> emtol = 100 >> ;for SD >> emstep = 0.1 >> ;for CG >> ;emstep = 0.001 >> >> nstcomm = 1 >> ns_type = grid >> rlist = 1 >> rcoulomb = 1.0 >> rvdw = 1.0 >> Tcoupl = no >> Pcoupl = no >> gen_vel = no >> >> >> Anwar >> >> ---------------------- >> Mohd Anwaruddin >> Project Assistant >> C/o DR.H.A.Nagarajaram >> Lab of Computational Biology and Bioinformatics >> Center for DNA Fingerprinting and Diagnostics(CDFD) >> Nacharam >> Hyderabad-500 076 >> INDIA. >> Tel: +91-8413-235467,68,69,70 ext 2019 >> anwar.m1 at gmail.com >> ----------------------- >> >> >> >> - >> >> _______________________________________________ >> gmx-users mailing list gmx-users at gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-request at gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From kwichapong at gmail.com Thu Sep 7 14:30:02 2006 From: kwichapong at gmail.com (kanin wichapong) Date: Thu, 7 Sep 2006 14:30:02 +0200 Subject: [gmx-users] Charge calculation in Gromacs Message-ID: <172bb8a80609070530q405f8fffh15b6cecdc7dcda30@mail.gmail.com> Dear All who may concern, I have some questions for the charge calculation in Gromacs, I used the forcefied ffG43a1 for the protein and inhibitors. Does the charge for the protein is the charge per residue? This forcefield is just for the polar H, right? For the nonpolar H, it will merge the H into the Heavy atom, right? I would like to know that does this force field also calculate the charge for the nonpolar H and then sum the charge with the heavy atom which it connects to or it doesn't calculate the charge for the nonpolar H? Does the charge of the Heavy atom is its own charge without sum together with the nonpolar H which connect to it? Moreover, I would like to know that if I would like to use quantum mechanics (qm) to calculate the charge for my inhibitor, what should be the method and the basis set to use to calculate for the charge to make it compiles with the ffG43a1 force fields? Thank you in advance for all of your help. Hope to hear from you soon With Best all regard Kanin Wichapong -------------- next part -------------- An HTML attachment was scrubbed... URL: From mark.abraham at anu.edu.au Thu Sep 7 15:27:02 2006 From: mark.abraham at anu.edu.au (Mark Abraham) Date: Thu, 7 Sep 2006 23:27:02 +1000 (EST) Subject: [gmx-users] Charge calculation in Gromacs In-Reply-To: <172bb8a80609070530q405f8fffh15b6cecdc7dcda30@mail.gmail.com> References: <172bb8a80609070530q405f8fffh15b6cecdc7dcda30@mail.gmail.com> Message-ID: <54994.150.203.145.27.1157635622.squirrel@sqmail.anu.edu.au> > Dear All who may concern, > I have some questions for the charge calculation in Gromacs, I used > the > forcefied ffG43a1 for the protein and inhibitors. Does the charge for the > protein is the charge per residue? The charge on a residue is the sum of the charges on the (united) atoms that make it up. The charge on a protein is the sum of the charges on the residues that make it up (or all of the atoms, obviously). The charge per residue is almost never considered, as it normally doesn't aid anybody understanding physical behaviour. Hope that answers your question, because I can't understand it. > This forcefield is just for the polar > H, > right? For the nonpolar H, it will merge the H into the Heavy atom, right? Don't know in this specific case, but there are such forcefields. > I > would like to know that does this force field also calculate the charge > for > the nonpolar H and then sum the charge with the heavy atom which it > connects > to or it doesn't calculate the charge for the nonpolar H? The charge on a united atom is just a number - as is the charge on a polar H, or any H in a non-united-atom force field. You can think of it as the sum of the charges on the multiple atoms it models if it helps. > Does the charge > of > the Heavy atom is its own charge without sum together with the nonpolar H > which connect to it? Moreover, I would like to know that if I would like > to > use quantum mechanics (qm) to calculate the charge for my inhibitor, what > should be the method and the basis set to use to calculate for the charge > to > make it compiles with the ffG43a1 force fields? Sounds like you should find the documentation (journal article?) for this force field and read it. Also some introductory material on how force fields work sounds like it might be worthwhile :-) Wanting to extend a force field you don't understand yet is a recipe for disaster... Mark From Alessandro at polymer.kth.se Thu Sep 7 15:55:59 2006 From: Alessandro at polymer.kth.se (Alessandro Mattozzi) Date: Thu, 7 Sep 2006 15:55:59 +0200 Subject: [gmx-users] Viscosity in PE Message-ID: Dear Gromacs-users I have already run some MD, both in NVT and NPT, of Polyethylene (1000 atoms-backbone). I would like to estimate the viscosity of my systems. Is it possible even if it is a rubbery solid? Which method is the most suitable? Regards Alessandro Mattozzi -------------- next part -------------- An HTML attachment was scrubbed... URL: From chris.neale at utoronto.ca Thu Sep 7 16:44:22 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Thu, 7 Sep 2006 10:44:22 -0400 Subject: [gmx-users] Simulation problem with extended membrane system! Message-ID: <1157640262.45003046de3bb@webmail.utoronto.ca> If you can't write a script, then do the minimization and equilibration with water frozen in the z dimension (freeze_groups = water; freeze_dim = n n y) or use constraints in the z dimension (posre.itp force constant 1000 along z and 0 along x and y). This will stop it from going into the membrane. Before you start, sort the initial PDB according to z (you could do this in excel), remove any waters that you don't want, resort according to original order, and run pdb2gmx. Note that pope.pdb does have a small cluster of waters in the membrane. From ecaballe at uoregon.edu Thu Sep 7 17:03:27 2006 From: ecaballe at uoregon.edu (Esther Caballero-Manrique) Date: Thu, 07 Sep 2006 08:03:27 -0700 Subject: [gmx-users] Viscosity in PE In-Reply-To: References: Message-ID: <450034BF.8080707@uoregon.edu> You can calculate it from the velocity autocorrelation function, which can be calculated using the g_velacc. The friction can be calculated from the integral of the velocity autocorrelation function (friction=3KbT/(integral of vacf)) and then the viscosity can be calculated using Stoke's equation (friction=6 x PI x visc x radius). But you need to have saved the velocities fairly often (say every 5 fs?). This came up recently in the mailing lists, you can search the velocity autocorrelation function. This method integrates the integral at time infinite (ie, see Morriss and Evan's book /Statistical Mechanics of Nonequilibrium Liquids, /now on the web @ http://rsc.anu.edu.au/~evans/evansmorrissbook.htm) which might or might not be a good approximation for your system. Otherwise you can do more sophisticated methods such as those outlined in chapter 6 of the manual. Hope it helps, Esther Esther Caballero-Manrique Guenza Group University of Oregon Eugene, OR usa 541-346-2485 Alessandro Mattozzi wrote: > > > Dear Gromacs-users > I have already run some MD, both in NVT and NPT, of Polyethylene (1000 > atoms-backbone). > I would like to estimate the viscosity of my systems. Is it possible > even if it is a rubbery solid? Which method is the most suitable? > Regards > > Alessandro Mattozzi > >------------------------------------------------------------------------ > >_______________________________________________ >gmx-users mailing list gmx-users at gromacs.org >http://www.gromacs.org/mailman/listinfo/gmx-users >Please don't post (un)subscribe requests to the list. Use the >www interface or send it to gmx-users-request at gromacs.org. >Can't post? Read http://www.gromacs.org/mailing_lists/users.php > From navratna.vajpai at unibas.ch Thu Sep 7 15:27:04 2006 From: navratna.vajpai at unibas.ch (Navratna Vajpai) Date: Thu, 7 Sep 2006 15:27:04 +0200 Subject: [gmx-users] Continue run Message-ID: <50C0C5F6-33F7-4217-ABDE-41E058FCC6B3@unibas.ch> Dear All.. to continue the run, as i understood, I modified the md.mdp and then use the .tpr and .trr for the further run. Can anyone suggest that it is the right way or not? actually in one of the tutorials note i have just found to change the options as -time $value -until $value. I was wondering whether my way is also OK or not. Thanks Nav ******************************************* Navratna Vajpai Ph. D student in Prof. Grzesiek's laboratory Department of Structural Biology Biozentrum, University of Basel Klingelbergstrasse 70, CH-4056 Basel, Switzerland. Phone- +41 61 267 2080(O) +41 78 744 0810(M) navratna.vajpai at unibas.ch -------------- next part -------------- An HTML attachment was scrubbed... URL: From melicher at cray.dbp.fmph.uniba.sk Thu Sep 7 17:58:32 2006 From: melicher at cray.dbp.fmph.uniba.sk (Milan Melichercik) Date: Thu, 7 Sep 2006 17:58:32 +0200 Subject: [gmx-users] Continue run In-Reply-To: <50C0C5F6-33F7-4217-ABDE-41E058FCC6B3@unibas.ch> References: <50C0C5F6-33F7-4217-ABDE-41E058FCC6B3@unibas.ch> Message-ID: <200609071758.33013.melicher@cray.dbp.fmph.uniba.sk> D?a ?t 7. September 2006 15:27 Navratna Vajpai nap?sal: > Dear All.. > to continue the run, as i understood, I modified the md.mdp and then > use the .tpr and .trr for the further run. Can anyone suggest that it > is the right way or not? actually in one of the tutorials note i have > just found to change the options as -time $value -until $value. > I was wondering whether my way is also OK or not. Nearly right, but you don't need to modify the .mdb file. If your simulation crashed, simply execute 'tpbconv -s your_file.tpr -f your_file.trr -o your_new_file.tpr' (or you can add -e your_file.edr for energy) - this will generate new .tpr, which you use by running mdrun - that will generate something like your_new_file.trr and you can join then by 'trjcat -f your_file.trr your_new_file.trr -o your_full_file.trr, which will contain the whole simulation. The -time $value generates .tpr, which will start simulation from $value time (normally it starts from the last possible positions, so this is in the most cases not necessary). -until and -extend parameters you can use for continuing finished simulation until the given time/for the given time. The parameters of the simulation is allways the same. I hope it will help. Milan From zgxjlx at gmail.com Thu Sep 7 18:11:05 2006 From: zgxjlx at gmail.com (liu xin) Date: Fri, 8 Sep 2006 00:11:05 +0800 Subject: [gmx-users] Re: Simulation problem with extended membrane system! In-Reply-To: <1157640262.45003046de3bb@webmail.utoronto.ca> References: <1157640262.45003046de3bb@webmail.utoronto.ca> Message-ID: Hello Chris So you mean to do a constrained MDS to let the lipids "fill the gaps" between the box edges and lipids, after that do a unconstrained MDS, then we'll get a fine structure, am I right? Thank you very much, I'll try that Xin Liu On 9/7/06, chris.neale at utoronto.ca wrote: > If you can't write a script, then do the minimization and equilibration with > water frozen in the z dimension (freeze_groups = water; freeze_dim = n n y) > or > use constraints in the z dimension (posre.itp force constant 1000 along z > and 0 > along x and y). This will stop it from going into the membrane. Before you > start, sort the initial PDB according to z (you could do this in excel), > remove > any waters that you don't want, resort according to original order, and run > pdb2gmx. Note that pope.pdb does have a small cluster of waters in the > membrane. > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > From spoel at xray.bmc.uu.se Thu Sep 7 19:36:34 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Thu, 07 Sep 2006 19:36:34 +0200 Subject: [gmx-users] Viscosity in PE In-Reply-To: <450034BF.8080707@uoregon.edu> References: <450034BF.8080707@uoregon.edu> Message-ID: <450058A2.609@xray.bmc.uu.se> Esther Caballero-Manrique wrote: > You can calculate it from the velocity autocorrelation function, which > can be calculated using the g_velacc. The friction can be calculated > from the integral of the velocity autocorrelation function > (friction=3KbT/(integral of vacf)) and then the viscosity can be > calculated using Stoke's equation (friction=6 x PI x visc x radius). But > you need to have saved the velocities fairly often (say every 5 fs?). > This came up recently in the mailing lists, you can search the velocity > autocorrelation function. This method integrates the integral at time > infinite (ie, see Morriss and Evan's book /Statistical Mechanics of > Nonequilibrium Liquids, /now on the web @ > http://rsc.anu.edu.au/~evans/evansmorrissbook.htm) which might or might > not be a good approximation for your system. Otherwise you can do more > sophisticated methods such as those outlined in chapter 6 of the manual. > Hope it helps, > Esther An alternative method that is implemented requires non-equibrium simulations. Check out @Article{Hess2002b, author = {B. Hess}, title = {Determining the shear viscosity of model liquids from molecular simulation}, journal = {J. Chem. Phys.}, year = 2002, volume = 116, pages = {209-217} } you have to set cos_acceleration in the mdp to e.g. 0.1 nm/ps^2 > > Esther Caballero-Manrique > Guenza Group > University of Oregon > Eugene, OR > usa > 541-346-2485 > Alessandro Mattozzi wrote: > >> >> >> Dear Gromacs-users >> I have already run some MD, both in NVT and NPT, of Polyethylene (1000 >> atoms-backbone). >> I would like to estimate the viscosity of my systems. Is it possible >> even if it is a rubbery solid? Which method is the most suitable? >> Regards >> >> Alessandro Mattozzi >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users at gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-request at gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From yappik4050 at yahoo.com Thu Sep 7 22:11:52 2006 From: yappik4050 at yahoo.com (Cherry Y. Yates) Date: Thu, 7 Sep 2006 13:11:52 -0700 (PDT) Subject: [gmx-users] how to exclude some atoms from coulomb interaction calculation? Message-ID: <20060907201152.26965.qmail@web56901.mail.re3.yahoo.com> Dear all, I did a massive MD simulation of nanostructure. In my calculation, over 80% atoms have zero charge and the main CPU time is devoted to Coulomb interaction. I wonder if anyone knows how to exclude these neutral atoms from Coublomb interaction so that a lot of CPU time will be saved. Many thanks, Cherry __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From fileti at iq.usp.br Thu Sep 7 23:18:25 2006 From: fileti at iq.usp.br (Eudes Fileti) Date: Thu, 7 Sep 2006 18:18:25 -0300 Subject: [gmx-users] Buckingham model for liquid of water Message-ID: <65e289a20609071418j6d746dd2tc09f3933db0193d8@mail.gmail.com> Dear gmx-ers I have attemped to use the potential of Buckingham to simulate the water liquid. However I did not find papers that present the parameters of the potential. Actually I found a paper that mixed parameters LJ (O...O) and Buckingham (O-H, O-O and H...O). Can anyone let me know if there is a optmized set parameters for the water with this potential ? Thanks eef -- ______________________________________ Eudes Eterno Fileti Centro de Ci?ncia Naturais e Humanas Universidade Federal do ABC Rua Santa Ad?lia, 166 CEP 09210-170 skype: eefileti -------------- next part -------------- An HTML attachment was scrubbed... URL: From maaren at home.nl Thu Sep 7 23:39:48 2006 From: maaren at home.nl (Paul van Maaren) Date: Thu, 7 Sep 2006 23:39:48 +0200 Subject: [gmx-users] Buckingham model for liquid of water In-Reply-To: <65e289a20609071418j6d746dd2tc09f3933db0193d8@mail.gmail.com> References: <65e289a20609071418j6d746dd2tc09f3933db0193d8@mail.gmail.com> Message-ID: <200609072339.48941.maaren@home.nl> On Thursday 07 September 2006 23:18, Eudes Fileti wrote: > Dear gmx-ers > I have attemped to use the potential of Buckingham > to simulate the water liquid. However I did not find > papers that present the parameters of the potential. > Actually I found a paper that mixed parameters LJ (O...O) > and Buckingham (O-H, O-O and H...O). > Can anyone let me know if there is a optmized set parameters > for the water with this potential ? The following article contains such a model: @Article{Errington1998a, author = {J. R. Errington and A. Z. Panagiotopoulos}, title = {A Fixed Point Charge Model for Water Optimized to the Vapor-Liquid Coexistence Properties}, journal = BTjpcb, year = 1998, volume = 102, pages = {7470-7475}, OPTabstract = {}, OPTnote = {}, doi = {http://dx.doi.org/} } -- Groeten, Paul van Maaren From chris.neale at utoronto.ca Fri Sep 8 03:46:01 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Thu, 7 Sep 2006 21:46:01 -0400 Subject: [gmx-users] Re: Simulation problem with extended membrane system! Message-ID: <1157679961.4500cb59b996b@webmail.utoronto.ca> Having actually looked back at my notes, here is what I did to extend pope.pdb into a larger system. However, the suggestion that I posted last time should work just as well. 1. Remove all waters 2. Duplicate the box until your heart's content. Make it larger than you actually want because the box will collapse to some extent. 3. MD with Z-only posre on lipid head groups (X and Y force components = zero). This step must be done with constant pressure (In this procedure, make sure to use isotropic pressure coupling so that the box max and min z don't come into contact with the membrane). NOTE for step 3: It is assumed that your edges line up with each other. Load the system into vmd and show periodic unit cells to make sure. If they line up poorly then I would find a new starting PDB. However, pope.pdb lines up well. 4. Adjust the z-dimension to what you want it to be, center your membrane in the z if you want to. 5. solvate the system. 6. Remove any waters that were placed within the membrane 7. energy minimize 8. posre run as before to allow the water to adjust to the membrane surfaces. However, during this run (and all the rest of the steps) I use semiisotropic Pcoupling. 9. equilibration phase without any position restraints 10. production run. If you are going to add protein, you could do that with the results of step 4 since most procedures involve stripping out any waters anyway. Again, the procedure that I outlined previously should work, but I have not tested that procedure, only this one. From gmx3 at hotmail.com Fri Sep 8 08:34:16 2006 From: gmx3 at hotmail.com (Berk Hess) Date: Fri, 08 Sep 2006 08:34:16 +0200 Subject: [gmx-users] Viscosity in PE In-Reply-To: <450058A2.609@xray.bmc.uu.se> Message-ID: >From: David van der Spoel >Reply-To: Discussion list for GROMACS users >To: Discussion list for GROMACS users >Subject: Re: [gmx-users] Viscosity in PE >Date: Thu, 07 Sep 2006 19:36:34 +0200 > >Esther Caballero-Manrique wrote: >>You can calculate it from the velocity autocorrelation function, which can >>be calculated using the g_velacc. The friction can be calculated from the >>integral of the velocity autocorrelation function (friction=3KbT/(integral >>of vacf)) and then the viscosity can be calculated using Stoke's equation >>(friction=6 x PI x visc x radius). But you need to have saved the >>velocities fairly often (say every 5 fs?). This came up recently in the >>mailing lists, you can search the velocity autocorrelation function. This >>method integrates the integral at time infinite (ie, see Morriss and >>Evan's book /Statistical Mechanics of Nonequilibrium Liquids, /now on the >>web @ http://rsc.anu.edu.au/~evans/evansmorrissbook.htm) which might or >>might not be a good approximation for your system. Otherwise you can do >>more sophisticated methods such as those outlined in chapter 6 of the >>manual. >>Hope it helps, >>Esther > >An alternative method that is implemented requires non-equibrium >simulations. Check out > >@Article{Hess2002b, > author = {B. Hess}, > title = {Determining the shear viscosity of model liquids from >molecular simulation}, > journal = {J. Chem. Phys.}, > year = 2002, > volume = 116, > pages = {209-217} >} > >you have to set cos_acceleration in the mdp to e.g. 0.1 nm/ps^2 In Gromacs viscosity calculations can be done with several methods, all of which are described in the paper mentioned above. But for PE-1000 it is not that straightforward as for a simple liquid. The system has very long relaxation times and the viscosity will be very non-linear in the shear rate. You should read some literature on viscosity calculations in polymer melts. Berk. From Alessandro at polymer.kth.se Fri Sep 8 09:30:50 2006 From: Alessandro at polymer.kth.se (Alessandro Mattozzi) Date: Fri, 8 Sep 2006 09:30:50 +0200 Subject: [gmx-users] Viscosity in PE References: Message-ID: Thanx! Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden -----Original Message----- From: gmx-users-bounces at gromacs.org on behalf of Berk Hess Sent: Fri 9/8/2006 8:34 AM To: gmx-users at gromacs.org Subject: Re: [gmx-users] Viscosity in PE >From: David van der Spoel >Reply-To: Discussion list for GROMACS users >To: Discussion list for GROMACS users >Subject: Re: [gmx-users] Viscosity in PE >Date: Thu, 07 Sep 2006 19:36:34 +0200 > >Esther Caballero-Manrique wrote: >>You can calculate it from the velocity autocorrelation function, which can >>be calculated using the g_velacc. The friction can be calculated from the >>integral of the velocity autocorrelation function (friction=3KbT/(integral >>of vacf)) and then the viscosity can be calculated using Stoke's equation >>(friction=6 x PI x visc x radius). But you need to have saved the >>velocities fairly often (say every 5 fs?). This came up recently in the >>mailing lists, you can search the velocity autocorrelation function. This >>method integrates the integral at time infinite (ie, see Morriss and >>Evan's book /Statistical Mechanics of Nonequilibrium Liquids, /now on the >>web @ http://rsc.anu.edu.au/~evans/evansmorrissbook.htm) which might or >>might not be a good approximation for your system. Otherwise you can do >>more sophisticated methods such as those outlined in chapter 6 of the >>manual. >>Hope it helps, >>Esther > >An alternative method that is implemented requires non-equibrium >simulations. Check out > >@Article{Hess2002b, > author = {B. Hess}, > title = {Determining the shear viscosity of model liquids from >molecular simulation}, > journal = {J. Chem. Phys.}, > year = 2002, > volume = 116, > pages = {209-217} >} > >you have to set cos_acceleration in the mdp to e.g. 0.1 nm/ps^2 In Gromacs viscosity calculations can be done with several methods, all of which are described in the paper mentioned above. But for PE-1000 it is not that straightforward as for a simple liquid. The system has very long relaxation times and the viscosity will be very non-linear in the shear rate. You should read some literature on viscosity calculations in polymer melts. Berk. _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -------------- next part -------------- A non-text attachment was scrubbed... Name: winmail.dat Type: application/ms-tnef Size: 3972 bytes Desc: not available URL: From gmx3 at hotmail.com Fri Sep 8 10:31:27 2006 From: gmx3 at hotmail.com (Berk Hess) Date: Fri, 08 Sep 2006 10:31:27 +0200 Subject: [gmx-users] Viscosity in PE In-Reply-To: <450058A2.609@xray.bmc.uu.se> Message-ID: >From: David van der Spoel >Reply-To: Discussion list for GROMACS users >To: Discussion list for GROMACS users >Subject: Re: [gmx-users] Viscosity in PE >Date: Thu, 07 Sep 2006 19:36:34 +0200 > >Esther Caballero-Manrique wrote: >>You can calculate it from the velocity autocorrelation function, which can >>be calculated using the g_velacc. The friction can be calculated from the >>integral of the velocity autocorrelation function (friction=3KbT/(integral >>of vacf)) and then the viscosity can be calculated using Stoke's equation >>(friction=6 x PI x visc x radius). But you need to have saved the >>velocities fairly often (say every 5 fs?). This came up recently in the >>mailing lists, you can search the velocity autocorrelation function. This >>method integrates the integral at time infinite (ie, see Morriss and >>Evan's book /Statistical Mechanics of Nonequilibrium Liquids, /now on the >>web @ http://rsc.anu.edu.au/~evans/evansmorrissbook.htm) which might or >>might not be a good approximation for your system. Otherwise you can do >>more sophisticated methods such as those outlined in chapter 6 of the >>manual. >>Hope it helps, >>Esther > >An alternative method that is implemented requires non-equibrium >simulations. Check out > >@Article{Hess2002b, > author = {B. Hess}, > title = {Determining the shear viscosity of model liquids from >molecular simulation}, > journal = {J. Chem. Phys.}, > year = 2002, > volume = 116, > pages = {209-217} >} > >you have to set cos_acceleration in the mdp to e.g. 0.1 nm/ps^2 In Gromacs viscosity calculations can be done with several methods, all of which are described in the paper mentioned above. But for PE-1000 it is not that straightforward as for a simple liquid. The system has very long relaxation times and the viscosity will be very non-linear in the shear rate. You should read some literature on viscosity calculations in polymer melts. Berk. From zgxjlx at gmail.com Fri Sep 8 10:35:25 2006 From: zgxjlx at gmail.com (liu xin) Date: Fri, 8 Sep 2006 16:35:25 +0800 Subject: [gmx-users] Re: Simulation problem with extended membrane system! In-Reply-To: <1157679961.4500cb59b996b@webmail.utoronto.ca> References: <1157679961.4500cb59b996b@webmail.utoronto.ca> Message-ID: Hi Chris Thank you for your note! According to your suggestion, I did a energy minimization and then a MDS with "freezegrps=SOL, freezedim=N, N, Y", the rest of the system were simulated with no constraint. This time I use semiisotropic pressure coupling with tau_p=5. The system will be equilibrated with water constrained for 1ns, do you think it's enough? The reason why I want to extend the system is because that I've got a GPCR, and I want to simulate it in a DPPC membrane environment, but the z dimension of the membrane, downloaded from Dr. Tielman's websit, was not large enough, when I align the protein to the z axis of the membrane I find the two ends of the protein are poking out of both water layers. Back to the previous question, after solvate the lipids in water, can I remove the water placed in the membrane with excel instead of script? Cause with editconf we can know the z dimension of the lipids_only system, let's say 6, so if I center the whole system with 0 0 0, the water molecules with z coordinates below 3 and above -3 will be excluded. If I'm right, I think excel can do it too, or the scripts have some advantages? Thank you again On 9/8/06, chris.neale at utoronto.ca wrote: > > Having actually looked back at my notes, here is what I did to extend > pope.pdb > into a larger system. However, the suggestion that I posted last time > should > work just as well. > > 1. Remove all waters > 2. Duplicate the box until your heart's content. Make it larger than you > actually want because the box will collapse to some extent. > 3. MD with Z-only posre on lipid head groups (X and Y force components = > zero). > This step must be done with constant pressure (In this procedure, make > sure to > use isotropic pressure coupling so that the box max and min z don't come > into > contact with the membrane). > > NOTE for step 3: It is assumed that your edges line up with each other. > Load the > system into vmd and show periodic unit cells to make sure. If they line up > poorly then I would find a new starting PDB. However, pope.pdb lines up > well. > > 4. Adjust the z-dimension to what you want it to be, center your membrane > in the > z if you want to. > 5. solvate the system. > 6. Remove any waters that were placed within the membrane > 7. energy minimize > 8. posre run as before to allow the water to adjust to the membrane > surfaces. > However, during this run (and all the rest of the steps) I use > semiisotropic > Pcoupling. > 9. equilibration phase without any position restraints > 10. production run. > > If you are going to add protein, you could do that with the results of > step 4 > since most procedures involve stripping out any waters anyway. > > Again, the procedure that I outlined previously should work, but I have > not > tested that procedure, only this one. > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -------------- next part -------------- An HTML attachment was scrubbed... URL: From spoel at xray.bmc.uu.se Fri Sep 8 11:02:52 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Fri, 08 Sep 2006 11:02:52 +0200 Subject: [gmx-users] how to exclude some atoms from coulomb interaction calculation? In-Reply-To: <20060907201152.26965.qmail@web56901.mail.re3.yahoo.com> References: <20060907201152.26965.qmail@web56901.mail.re3.yahoo.com> Message-ID: <450131BC.3000103@xray.bmc.uu.se> Cherry Y. Yates wrote: > Dear all, > > I did a massive MD simulation of nanostructure. In my calculation, over > 80% atoms have zero charge and the main CPU time is devoted to Coulomb > interaction. I wonder if anyone knows how to exclude these neutral atoms > from Coublomb interaction so that a lot of CPU time will be saved. > They are excluded already. GROMACS does not compute nonbonded interactions when the result is zero. This can be due to charges or LJ parameters being zero. > Many thanks, > > Cherry > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From zzhwise1 at 163.com Fri Sep 8 11:24:11 2006 From: zzhwise1 at 163.com (zzhwise1) Date: Fri, 8 Sep 2006 17:24:11 +0800 (CST) Subject: [gmx-users] why the mdrun stop Message-ID: <450136BB.00006D.19374@bj163app51.163.com> hello ,everyone I have two problems: (1)my model is compost of 36 long chain of CH3(CH2)14COOH ,and use the frocefiled of ffgmx, but the mdrun can only going to the 2th step,and the some chains change large (2)can this program do the nanotribology of monolayer? thanks advanced! wait for your answer! your friend -------------- next part -------------- An HTML attachment was scrubbed... URL: From spoel at xray.bmc.uu.se Fri Sep 8 13:05:02 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Fri, 08 Sep 2006 13:05:02 +0200 Subject: [gmx-users] why the mdrun stop In-Reply-To: <450136BB.00006D.19374@bj163app51.163.com> References: <450136BB.00006D.19374@bj163app51.163.com> Message-ID: <45014E5E.5040004@xray.bmc.uu.se> zzhwise1 wrote: > > hello ,everyone > I have two problems: > (1)my model is compost of 36 long chain of CH3(CH2)14COOH ,and use the > frocefiled of ffgmx, > but the mdrun can only going to the 2th step,and the some chains change > large > (2)can this program do the nanotribology of monolayer? > thanks advanced! > wait for your answer! check your starting structure. start with one molecule, minimize, do MD and then go to 36 molecules. > your friend > > > > > > > > > > ? ? ? ? ? ? ? ? ? ( ? ) > ? ? ? ? ? ! ? ? ? ? ? 5800 ? ? MM ? ? ? ? ? ( ? ? ) > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From ikass at cc.huji.ac.il Fri Sep 8 11:50:36 2006 From: ikass at cc.huji.ac.il (Itamar Kass) Date: Fri, 8 Sep 2006 12:50:36 +0300 Subject: [gmx-users] why the mdrun stop In-Reply-To: <450136BB.00006D.19374@bj163app51.163.com> References: <450136BB.00006D.19374@bj163app51.163.com> Message-ID: <1157709036.45013cec0351d@webmail.huji.ac.il> Shalom, You did not mention if you did energy minimization or other preliminary steps before your MD. If not, this might solve the problem. Best, Itamar. Quoting zzhwise1 : > > hello ,everyone > I have two problems: > (1)my model is compost of 36 long chain of CH3(CH2)14COOH ,and use the > frocefiled of ffgmx, > but the mdrun can only going to the 2th step,and the some chains change large > (2)can this program do the nanotribology of monolayer? > thanks advanced! > wait for your answer! > your friend > > =========================================== | Itamar Kass | The Alexander Silberman | Institute of Life Sciences | Department of Biological Chemistry | The Hebrew University, Givat-Ram | Jerusalem, 91904, Israel | Tel: +972-(0)2-6585194 | Fax: +972-(0)2-6584329 | Email: ikass at cc.huji.ac.il ============================================ ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From una.bjarnadottir at ucd.ie Fri Sep 8 14:21:02 2006 From: una.bjarnadottir at ucd.ie (Una Bjarnadottir) Date: Fri, 08 Sep 2006 13:21:02 +0100 Subject: [gmx-users] genion causing atom to be in multiple T-Coupling groups In-Reply-To: <20060905213839.51D922407F@xray.bmc.uu.se> References: <20060905213839.51D922407F@xray.bmc.uu.se> Message-ID: <4501602E.5030802@ucd.ie> Dear Users, I'm trying to neutralize my system adding 3 Cl ions with genion and when running grompp again with the new generated .gro file I get this error: Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1) which is the last water atom (total in system 33003) and groups 15 and 1 are Cl and protein groups if I on the other hand do not neutralize the system the run goes fine! So there is something wrong with how the genion works for me. I followed the tutorial and chose the SOL group and water molecules were replaced by the Cl ions. Than I modifyed the .top file and took 3 sol molecules and added the 3 ions. _* *_Best regards for any help, Una Bjarnadottir _* .top before: *_; Include generic topology for ions #include "ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound #mols Protein_E 1 Protein_I 1 Protein_A 1 SOL 9719 _*.top after*_ ; Include generic topology for ions #include "ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound #mols Protein_E 1 Protein_I 1 Protein_A 1 SOL 9716 CL- 3 _*These are my commands:*_ # #Run grompp # emfile_mdpfile='em.mdp' emout='em_out.mdp' structure_file='em.tpr' os.system('/usr/local/bin/grompp -f '+emfile_mdpfile+ ' -po ' +emout+ ' -c ' +water_grofile+ ' -o ' +structure_file+ ' -p ' +topologyfile) # #Run genion # ion_out='ion.gro' os.system('/usr/local/bin/genion -s '+structure_file+ ' -o ' +ion_out+ ' -nname Cl -nn 3') # #Run grompp # structure_file_after_genion='em_genion.tpr' os.system('/usr/local/bin/grompp -f '+emfile_mdpfile+ ' -po ' +emout+ ' -c ' +ion_out+ ' -o ' +structure_file_after_genion+ ' -p ' +topologyfile) From martin.hoefling at gmx.de Fri Sep 8 18:05:38 2006 From: martin.hoefling at gmx.de (Martin =?iso-8859-1?q?H=F6fling?=) Date: Fri, 8 Sep 2006 18:05:38 +0200 Subject: [gmx-users] Splitting one run Message-ID: <200609081805.38965.martin.hoefling@gmx.de> Hi there, I heard that there's an unofficial script to split one run in several small ones. Anyone of you remembers the topic so that I can search for it? Regards Martin From spoel at xray.bmc.uu.se Fri Sep 8 18:09:52 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Fri, 08 Sep 2006 18:09:52 +0200 Subject: [Fwd: Re: Re: [gmx-users] why the mdrun stop] Message-ID: <450195D0.5060902@xray.bmc.uu.se> -------- Original Message -------- Subject: Re: Re: [gmx-users] why the mdrun stop Date: Fri, 8 Sep 2006 21:58:02 +0800 (CST) From: zzhwise1 To: david van der spoel References: <450136BB.00006D.19374 at bj163app51.163.com> <45014E5E.5040004 at xray.bmc.uu.se> I try 3 long chains but I don't konw why the program do not allow the bond to rotation 30 or more degree? does it the case of the wrong ff or wrong integrate ? ------------------------------------------------------------------------ -----????----- ???:"David van der Spoel" ????:2006-09-08 19:05:02 ???:"Discussion list for GROMACS users" ??:(?) ??:Re: [gmx-users] why the mdrun stop zzhwise1 wrote: > > hello ,everyone > I have two problems: > (1)my model is compost of 36 long chain of CH3(CH2)14COOH ,and use the > frocefiled of ffgmx, > but the mdrun can only going to the 2th step,and the some chains change > large > (2)can this program do the nanotribology of monolayer? > thanks advanced! > wait for your answer! check your starting structure. start with one molecule, minimize, do MD and then go to 36 molecules. > your friend > > > > > > > > > > ? ? ? ? ? ? ? ? ? ( ? ) > ? ? ? ? ? ! ? ? ? ? ? 5800 ? ? MM ? ? ? ? ? ( ? ? ) > ,597,58&cid=29985,198,1&sid=32501&show=ignore&url=http://www.taobao.com/vertical/lady/pro.php> > > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ? ? ? ? ? ? ? ? ? ( ? ) ? ? ? ? ? ! ? ? ? ? ? 5800 ? ? MM ? ? ? ? ? ( ? ? ) -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ -------------- next part -------------- A non-text attachment was scrubbed... Name: CHOXIUGAI.mdp Type: application/octet-stream Size: 1261 bytes Desc: not available URL: From chris.neale at utoronto.ca Fri Sep 8 18:35:05 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Fri, 8 Sep 2006 12:35:05 -0400 Subject: [gmx-users] Re: Simulation problem with extended membrane system! Message-ID: <1157733305.45019bb953127@webmail.utoronto.ca> >According to your suggestion, I did a energy minimization and then a MDS >with "freezegrps=SOL, freezedim=N, N, Y", the rest of the system were >simulated with no constraint. This time I use semiisotropic pressure >coupling with tau_p=5. The system will be equilibrated with water >constrained for 1ns, do you think it's enough? It will be more than enough. Use vmd to watch the trajectory. It's important actually look at the structures. >The reason why I want to extend the system is because that I've got a GPCR, >and I want to simulate it in a DPPC membrane environment, but the z >dimension of the membrane, downloaded from Dr. Tielman's websit, was not >large enough, when I align the protein to the z axis of the membrane I find >the two ends of the protein are poking out of both water layers. In this case you may not need to extend the lipid. Why not just use editconf to increase the z dimension while keeping the x and y constant. Then insert your protein, re-solvate, re-equilibrate, and your into production. If your lipid takes up a maximum amout of space D in the xy-plane, then x and y need only be equal to [D + 2*max(LJ cutoff, Coulombic real-space cutoff) + some extra amount in case the protein fluctuations make it larger during the simulation]. >Back to the previous question, after solvate the lipids in water, can I >remove the water placed in the membrane with excel instead of script? Cause >with editconf we can know the z dimension of the lipids_only system, let's >say 6, so if I center the whole system with 0 0 0, the water molecules with >z coordinates below 3 and above -3 will be excluded. If I'm right, I think >excel can do it too, or the scripts have some advantages? Sure you can use excel, but I am not sure how that is going to affect your formatting or how gromacs responds to formatting (i.e. spaces / tabs / the number of each) So scrips have 2 advantages: 1)formatting is easily maintained, 2)if you need to do it a second time you just type one command. After using excel (or a script) make sure to update you topology file to indicate the number of waters. From JeffreyCopps at creighton.edu Fri Sep 8 18:46:22 2006 From: JeffreyCopps at creighton.edu (Copps, Jeffrey) Date: Fri, 8 Sep 2006 11:46:22 -0500 Subject: [gmx-users] TFE .gro files Message-ID: Hello all, Does anyone have TFE (trifluoroethanol) .gro files that they might be willing to share? Or, barring that, can anyone tell me how to create a solvent .gro file? Much thanks, Jeff Copps -------------- next part -------------- An HTML attachment was scrubbed... URL: From jianhuitian at gmail.com Fri Sep 8 19:26:45 2006 From: jianhuitian at gmail.com (Jianhui Tian) Date: Fri, 8 Sep 2006 13:26:45 -0400 Subject: [gmx-users] Coulomb 1-4 interactions Message-ID: <1ea820a30609081026o7fe5f43bsfa010f91afa1f432@mail.gmail.com> Hi gmx-users: I am running a comparison between AMBER and Gromacs for a AOT system. First I created the AMBER force field and then transformed it to Gromacs force field. I did 1 step of MD respectively in AMBER and Gromacs with the same configuration. All the energy terms including bond, angle, dihedral, LJ (SR), LJ (14) and Coulomb (SR) are the same with each other between the two runs except the Coulomb (14) interaction. What might be the reason for this? I have totally no idea. Because the LJ (14) and Coulomb (14) calculation use the same 1-4 pairs in Gromacs, the LJ (14) is the same which means the 1-4 pairs are the same between AMBER and Gromacs. The Coulomb (SR) is the same which means the charges are the same between AMBER and Gromacs. (I also checked these two things explicitly between AMBER and Gromacs.) How could the Coulomb (14) be different then? Does any one have any idea about how the coulomb (14) interactions are calculated in AMBER and Gromacs? Thanks a lot. Best Regards, Justin -------------- next part -------------- An HTML attachment was scrubbed... URL: From rsugitani at gmail.com Fri Sep 8 19:41:57 2006 From: rsugitani at gmail.com (Ryogo Sugitani) Date: Fri, 8 Sep 2006 10:41:57 -0700 Subject: [gmx-users] Coulomb 1-4 interactions In-Reply-To: <1ea820a30609081026o7fe5f43bsfa010f91afa1f432@mail.gmail.com> References: <1ea820a30609081026o7fe5f43bsfa010f91afa1f432@mail.gmail.com> Message-ID: <20060908104157.710635.1983f9de@ucdavis.edu> Justin, What is your fudgeQQ value in ffamberXX.itp? This value (I think the default is 0.8333) should be the reciprocal of scaling factor used in Amber's input file (I think the default is 1.200). Check amber's manual specific parameter name for it. (I don't remember off my head right now.) Best, Ryogo On Fri, 8 Sep 2006 13:26:45 -0400, Jianhui Tian wrote: > Hi gmx-users: > > I am running a comparison between AMBER and Gromacs for a AOT system. > First I created the AMBER force field and then transformed it to > Gromacs force field. I did 1 step of MD respectively in AMBER and > Gromacs with the same configuration. All the energy terms including > bond, angle, dihedral, LJ (SR), LJ (14) and Coulomb (SR) are the same > with each other between the two runs except the Coulomb (14) > interaction. What might be the reason for this? I have totally no > idea. Because the LJ (14) and Coulomb (14) calculation use the same > 1-4 pairs in Gromacs, the LJ (14) is the same which means the 1-4 > pairs are the same between AMBER and Gromacs. The Coulomb (SR) is the > same which means the charges are the same between AMBER and Gromacs. > (I also checked these two things explicitly between AMBER and > Gromacs.) How could the Coulomb (14) be different then? Does any one > have any idea about how the coulomb (14) interactions are calculated > in AMBER and Gromacs? Thanks a lot. > > Best Regards, > Justin > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php From mark.abraham at anu.edu.au Sat Sep 9 01:51:12 2006 From: mark.abraham at anu.edu.au (Mark Abraham) Date: Sat, 9 Sep 2006 09:51:12 +1000 (EST) Subject: [gmx-users] Coulomb 1-4 interactions In-Reply-To: <1ea820a30609081026o7fe5f43bsfa010f91afa1f432@mail.gmail.com> References: <1ea820a30609081026o7fe5f43bsfa010f91afa1f432@mail.gmail.com> Message-ID: <2098.150.101.115.79.1157759472.squirrel@sqmail.anu.edu.au> > Hi gmx-users: > > I am running a comparison between AMBER and Gromacs for a AOT system. > First > I created the AMBER force field and then transformed it to Gromacs force > field. There are existing ports that you can find in the User Contributions section of the GROMACS webpage. Comparing yours with theirs may well be instructive for somebody. > I did 1 step of MD respectively in AMBER and Gromacs with the same > configuration. All the energy terms including bond, angle, dihedral, LJ > (SR), LJ (14) and Coulomb (SR) are the same with each other between the > two > runs except the Coulomb (14) interaction. What might be the reason for > this? Various force fields routinely scale this interaction. Check the papers that describe the implementation of the AMBER force field for information here. Then read the GROMACS manual to work out how to implement the same. > I have totally no idea. Because the LJ (14) and Coulomb (14) calculation > use > the same 1-4 pairs in Gromacs, the LJ (14) is the same which means the 1-4 > pairs are the same between AMBER and Gromacs. The Coulomb (SR) is the same > which means the charges are the same between AMBER and Gromacs. (I also > checked these two things explicitly between AMBER and Gromacs.) How could > the Coulomb (14) be different then? Does any one have any idea about how > the > coulomb (14) interactions are calculated in AMBER and Gromacs? Thanks a > lot. See above - read the original papers. Mark From zzhwise1 at 163.com Sat Sep 9 02:07:26 2006 From: zzhwise1 at 163.com (zzhwise1) Date: Sat, 9 Sep 2006 08:07:26 +0800 (CST) Subject: [gmx-users] can the GMX model the monolayer frict ion ? Message-ID: <450205BE.00006E.25874@bj163app51.163.com> hello everyone I want to know whether GMX can simulate the LB monolayer or selfassemble monolayer on base ?if can not ,could advise one to me? thanks! -------------- next part -------------- An HTML attachment was scrubbed... URL: From mark.abraham at anu.edu.au Sat Sep 9 06:59:14 2006 From: mark.abraham at anu.edu.au (Mark Abraham) Date: Sat, 9 Sep 2006 14:59:14 +1000 (EST) Subject: [gmx-users] can the GMX model the monolayer frict ion ? In-Reply-To: <450205BE.00006E.25874@bj163app51.163.com> References: <450205BE.00006E.25874@bj163app51.163.com> Message-ID: <1283.150.101.115.79.1157777954.squirrel@sqmail.anu.edu.au> > > hello everyone > I want to know whether GMX can simulate the LB monolayer or > selfassemble monolayer on base ?if can not ,could advise one to me? > thanks! Yes it is mathematically capable of doing that. You would know this, and a whole lot more, if you read the GROMACS webpage thoroughly http://www.gromacs.org/ Mark From ymr79in at yahoo.co.in Sat Sep 9 08:30:01 2006 From: ymr79in at yahoo.co.in (Ragothaman Yennamalli) Date: Sat, 9 Sep 2006 07:30:01 +0100 (BST) Subject: [gmx-users] LINCS warning Message-ID: <20060909063001.73489.qmail@web8903.mail.in.yahoo.com> Dear all, I have a query, 1. Are two trajectories comparable if each one of them has been run in a different version of gromacs? Eg, v3.2 and v3.3. Thanks in advance, Regards, Raghu ************************************** Y. M. Ragothaman, Research Scholar, Centre for Computational Biology and Bioinformatics, School of Information Technology, Jawaharlal Nehru University, New Delhi - 110067. Telephone: 91-11-26717568, 26717585 Facsimile: 91-11-26717586 ************************************** __________________________________________________________ Yahoo! India Answers: Share what you know. Learn something new http://in.answers.yahoo.com/ From ymr79in at yahoo.co.in Sat Sep 9 09:13:27 2006 From: ymr79in at yahoo.co.in (Ragothaman Yennamalli) Date: Sat, 9 Sep 2006 08:13:27 +0100 (BST) Subject: [gmx-users] Gromacs version Message-ID: <20060909071327.81463.qmail@web8906.mail.in.yahoo.com> Dear all, I have a query, 1. Are two trajectories comparable if each one of them has been run in a different version of gromacs? Eg, v3.2 and v3.3. Thanks in advance, Regards, Raghu ************************************** Y. M. Ragothaman, Research Scholar, Centre for Computational Biology and Bioinformatics, School of Information Technology, Jawaharlal Nehru University, New Delhi - 110067. Telephone: 91-11-26717568, 26717585 Facsimile: 91-11-26717586 ************************************** __________________________________________________________ Yahoo! India Answers: Share what you know. Learn something new http://in.answers.yahoo.com/ From mark.abraham at anu.edu.au Sat Sep 9 09:15:55 2006 From: mark.abraham at anu.edu.au (Mark Abraham) Date: Sat, 9 Sep 2006 17:15:55 +1000 (EST) Subject: [gmx-users] LINCS warning In-Reply-To: <20060909063001.73489.qmail@web8903.mail.in.yahoo.com> References: <20060909063001.73489.qmail@web8903.mail.in.yahoo.com> Message-ID: <1378.150.101.115.79.1157786155.squirrel@sqmail.anu.edu.au> > Dear all, > I have a query, > 1. Are two trajectories comparable if each one of them > has been run in a different version of gromacs? Eg, > v3.2 and v3.3. Define "comparable". If you mean are they sampling the same thermodynamic ensemble, then the answer is yes if you used the same algorithms. If you mean are they numerically identical, the answer is no. Round-off errors from different order of summation, etc. will cause tiny differences that magnify chaotically. Mark From cxing at ucdavis.edu Sat Sep 9 09:19:21 2006 From: cxing at ucdavis.edu (Chenyue Xing) Date: Sat, 9 Sep 2006 00:19:21 -0700 Subject: [gmx-users] Gromacs version In-Reply-To: <20060909071327.81463.qmail@web8906.mail.in.yahoo.com> References: <20060909071327.81463.qmail@web8906.mail.in.yahoo.com> Message-ID: I think the statistical reserves but the two trajectories are not exactly the same. On 9/9/06, Ragothaman Yennamalli wrote: > > Dear all, > I have a query, > 1. Are two trajectories comparable if each one of them > has been run in a different version of gromacs? Eg, > v3.2 and v3.3. > > Thanks in advance, > Regards, > Raghu > > ************************************** > Y. M. Ragothaman, > Research Scholar, > Centre for Computational Biology and Bioinformatics, > School of Information Technology, > Jawaharlal Nehru University, > New Delhi - 110067. > > Telephone: 91-11-26717568, 26717585 > Facsimile: 91-11-26717586 > ************************************** > > > > __________________________________________________________ > Yahoo! India Answers: Share what you know. Learn something new > http://in.answers.yahoo.com/ > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -------------- next part -------------- An HTML attachment was scrubbed... URL: From petrucci86 at vip.sina.com Sat Sep 9 11:09:32 2006 From: petrucci86 at vip.sina.com (C.W. Liang) Date: Sat, 9 Sep 2006 17:09:32 +0800 Subject: [gmx-users] problem with dimer simulation ! Message-ID: <000c01c6d3ef$aca225f0$e5fd89dd@mychat44e50e4f> hi, all user: i performed the dimer simulation, and want to realize the interaction between two peptides. but frequently, i encountered this kind of problem: sometimes peptides moved out of the box, and sometimes they jumped back. i have tried so many way to pull them back with trjconv command, but still cause some unexpected problem. for example, peptides break to many parts ( with -pbc whole ) or diffuse out of box gradually ( with -pbc nojump ) with -ur or -center still not the trajectory i really want. i think maybe there are some tricks to perform. any suggestions for me ? thanks sooooooooooo much! -------------- next part -------------- An HTML attachment was scrubbed... URL: From kay.gottschalk at physik.uni-muenchen.de Sat Sep 9 17:42:34 2006 From: kay.gottschalk at physik.uni-muenchen.de (Kay Gottschalk) Date: Sat, 9 Sep 2006 17:42:34 +0200 Subject: [gmx-users] problem with dimer simulation ! In-Reply-To: <000c01c6d3ef$aca225f0$e5fd89dd@mychat44e50e4f> References: <000c01c6d3ef$aca225f0$e5fd89dd@mychat44e50e4f> Message-ID: try - cluster, and then as cluster group protein. Kay. On Sep 9, 2006, at 11:09 AM, C.W. Liang wrote: > hi, all user: > > i performed the dimer simulation, and want to realize the > interaction between two peptides. > but frequently, i encountered this kind of problem: sometimes > peptides moved out of the box, and sometimes they jumped back. > i have tried so many way to pull them back with trjconv command, > but still cause some unexpected problem. > for example, peptides break to many parts ( with -pbc whole ) or > diffuse out of box gradually ( with -pbc nojump ) > with -ur or -center still not the trajectory i really want. i think > maybe there are some tricks to perform. > any suggestions for me ? thanks sooooooooooo much! > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -------------- next part -------------- An HTML attachment was scrubbed... URL: From d.s.mueller at rug.nl Sun Sep 10 01:59:20 2006 From: d.s.mueller at rug.nl (Daniela S. =?ISO-8859-1?Q?M=FCller?=) Date: Sun, 10 Sep 2006 01:59:20 +0200 Subject: [gmx-users] LINCS warning In-Reply-To: <1378.150.101.115.79.1157786155.squirrel@sqmail.anu.edu.au> References: <20060909063001.73489.qmail@web8903.mail.in.yahoo.com> <1378.150.101.115.79.1157786155.squirrel@sqmail.anu.edu.au> Message-ID: hi raghu, in version 3.3 some bugs have been fixed, which you can read on the gromacs website. E.g. the temperature coupling algorithm has been modified, which means that this thermodynamical property is evaluated and assigned differently than in v3.2. This will change your simulations totally, you certainly won't be getting the same trajectories. In any case it's difficult to compare different runs if at the same time you are comparing different softwares. daniela On Sat, 9 Sep 2006 17:15:55 +1000 (EST) "Mark Abraham" wrote: >> Dear all, >> I have a query, >> 1. Are two trajectories comparable if each one of them >> has been run in a different version of gromacs? Eg, >> v3.2 and v3.3. > > Define "comparable". If you mean are they sampling the >same thermodynamic > ensemble, then the answer is yes if you used the same >algorithms. If you > mean are they numerically identical, the answer is no. >Round-off errors > from different order of summation, etc. will cause tiny >differences that > magnify chaotically. > > Mark -- Daniela S. M?ller Molecular Dynamics (MD) Groningen Biomolecular Sciences and Biotechnology Institute (GBB) MD group website: http://www.rug.nl/gbb/md Address: Daniela S. Mueller Molecular Dynamics group Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands email: D.S.Mueller at rug.nl From yanmaocai at 126.com Sun Sep 10 04:47:51 2006 From: yanmaocai at 126.com (Mao-Cai Yan) Date: Sun, 10 Sep 2006 10:47:51 +0800 (CST) Subject: [gmx-users] May I use "-b" and "-e" in the cosine con tent calculation of PC? Message-ID: <45037CD7.000033.15774@bj126app14.126.com> Hi dear friends, I just made an essential dynamics of 5ns; I calculated the cosine content of PC1 by using g_analyze -f proj5ns.xvg -cc proj5ns_cc.xvg it gave: "Cosine content of set 1 with 0.5 periods: 0.749969" the value is rather too high. However, I found that only trajectory between 3300~3890 ps is useful, so I calculated the cosine content during this period using g_analyze -f proj5ns.xvg -cc proj5ns_cc.xvg -b 3300 -e 3890 and it gave: "Cosine content of set 1 with 0.5 periods: 0.297911" I want to know whether the essential dynamics is meaningful? The cosine content of whole 5 ns is relative high, does it mean that the whole trajectory is not meaningful? In another word, is it reasonable to use "-b" and "-e" in the cosine content calculation? Thanks. Stanley Yan -------------- next part -------------- An HTML attachment was scrubbed... URL: From p.biswas at csuohio.edu Sun Sep 10 17:37:00 2006 From: p.biswas at csuohio.edu (Pradip K Biswas) Date: Sun, 10 Sep 2006 11:37:00 -0400 Subject: [gmx-users] Re: Query on Gromacs-CPMD QMMM Interface Message-ID: Hi Sandeep, To compile gmx-3.3.1_qmmm-1.3, the configure option --with-qmmm-cpmd does not require CPMD to be compiled and installed beforehand. The preprocessor flag just includes the calls for the interface to CPMD functions available inside gmx-3.3.1_qmmm-1.3. You can compile gmx-3.3.1_qmmm-1.3 independently. best, pb. From chris.neale at utoronto.ca Sun Sep 10 20:56:48 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Sun, 10 Sep 2006 14:56:48 -0400 Subject: [gmx-users] lincs regular output Message-ID: <1157914608.45045ff01fc85@webmail.utoronto.ca> When using LINCS, I get an output message at the frequency of nstlog (which makes me think that it is ok and not an error). Can anybody confirm that this is regular output? Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.135628 3 4 0.019061 After LINCS 0.000007 33 34 0.000002 This is a message that I get even when I don't get any complaining about rotation greater then 30deg. Thanks. I am sure that this has been touched on before, but there is so much discussion about lincs that my searches didn't lead me anywhere useful. From mark.abraham at anu.edu.au Sun Sep 10 23:03:32 2006 From: mark.abraham at anu.edu.au (Mark Abraham) Date: Mon, 11 Sep 2006 07:03:32 +1000 (EST) Subject: [gmx-users] lincs regular output In-Reply-To: <1157914608.45045ff01fc85@webmail.utoronto.ca> References: <1157914608.45045ff01fc85@webmail.utoronto.ca> Message-ID: <58827.150.203.145.27.1157922212.squirrel@sqmail.anu.edu.au> > When using LINCS, I get an output message at the frequency of nstlog > (which > makes me think that it is ok and not an error). Can anybody confirm that > this is > regular output? Yup, that's normal. Mark From spoel at xray.bmc.uu.se Mon Sep 11 00:51:56 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Sun, 10 Sep 2006 15:51:56 -0700 Subject: [gmx-users] May I use "-b" and "-e" in the cosine con tent calculation of PC? In-Reply-To: <45037CD7.000033.15774@bj126app14.126.com> References: <45037CD7.000033.15774@bj126app14.126.com> Message-ID: <4504970C.6040704@xray.bmc.uu.se> Mao-Cai Yan wrote: > Hi dear friends, > > I just made an essential dynamics of 5ns; I calculated the cosine > content of PC1 by using > g_analyze -f proj5ns.xvg -cc proj5ns_cc.xvg > it gave: "Cosine content of set 1 with 0.5 periods: 0.749969" > the value is rather too high. > > However, I found that only trajectory between 3300~3890 ps is useful, so > I calculated the cosine content during this period using > g_analyze -f proj5ns.xvg -cc proj5ns_cc.xvg -b 3300 -e 3890 > and it gave: "Cosine content of set 1 with 0.5 periods: 0.297911" > > I want to know whether the essential dynamics is meaningful? The cosine > content of whole 5 ns is relative high, does it mean that the whole > trajectory is not meaningful? In another word, is it reasonable to use > "-b" and "-e" in the cosine content calculation? > What do you mean only a fraction is useful? First check for equilibration (energy, rmsd etc.) then do the ED sampling after that, for a period that is considerably longer than the equilibration, e.g. an order of magnitude. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From spoel at xray.bmc.uu.se Mon Sep 11 02:58:26 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Sun, 10 Sep 2006 17:58:26 -0700 Subject: [gmx-users] Re: Thanks! In-Reply-To: <4504486F.4090601@hv.se> References: <44ED8217.2040803@hv.se> <44ED86B0.20603@xray.bmc.uu.se> <4504486F.4090601@hv.se> Message-ID: <4504B4B2.2050701@xray.bmc.uu.se> Steven Kirk wrote: > Ok yes, they use the trick of giving the shell a mass of 0.4 amu and > reducing the standard oxygen mass by the same amount. > > When I solvate my macromolecule with the equilibrated water model, > however, I get convergence to machine precision with large (E+06) forces > in the EM stage, and PR and full MD runs start OK but after about 70 x > 0.001ps mdrun_d throws lots of LINCS errors and segfaults. The problem > doesn't just lie on one water molecule - I tried deleting the water > molecule causing the problem, but there was just another one somewhere > else to take its place. > > Have you seen any behaviour like this in any of your shell water > simulations? the problem is most likely due to incompatible force fields, for instance because the hydrogen atoms do not carry a vanderwaals interaction. you don't say what the nature of the macromolecule is or the force field that you use. check what kind of interactions causes this; the general solution would be to have a polarizable FF for the macromolecule as well. > > Any advice gratefully received, > > Regards, > Steve Kirk -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From spoel at xray.bmc.uu.se Mon Sep 11 03:02:50 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Sun, 10 Sep 2006 18:02:50 -0700 Subject: [gmx-users] TFE .gro files In-Reply-To: References: Message-ID: <4504B5BA.2050106@xray.bmc.uu.se> Copps, Jeffrey wrote: > > Hello all, > > Does anyone have TFE (trifluoroethanol) .gro files that they might > be willing to share? Or, barring that, can anyone tell me how to create > a solvent .gro file? > > Much thanks, > > Jeff Copps > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php how about the united atom one in the share/gromacs/top directory? otherwise, use prodrg followed by genconf and pressure coupled MD. -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From yanmaocai at 126.com Mon Sep 11 03:20:43 2006 From: yanmaocai at 126.com (M. Yan) Date: Mon, 11 Sep 2006 09:20:43 +0800 (CST) Subject: [gmx-users] May I use "-b" and "- e" in the cosine con tent calculation of PC? Message-ID: <4504B9EB.000032.24755@bj126app25.126.com> Hi, In fact I simulated 30 nanoseconds, but I found the system reached equilibrium at 4.4 ns (by analyzing RMSD, Energy and visualizing, etc.) and did not change significantly in the last 25 ns. Thus I want to do an essential dynamics for the first 5 ns. I also calculated the covariance matrix for the whole 30 nanoseconds, but the cosine content of PC1 is still as high as 0.710. However, MD simulation longer than 30 ns is beyond our compute ability. Then what shall I do? Thanks. Original message:"David van der Spoel" Sent:2006-09-11 06:51:56 To: "Discussion list for GROMACS users" Object:Re: [gmx-users] May I use "-b" and "-e" in the cosine con tent calculation of PC? Mao-Cai Yan wrote: > Hi dear friends, > > I just made an essential dynamics of 5ns; I calculated the cosine > content of PC1 by using > g_analyze -f proj5ns.xvg -cc proj5ns_cc.xvg > it gave: "Cosine content of set 1 with 0.5 periods: 0.749969" > the value is rather too high. > > However, I found that only trajectory between 3300~3890 ps is useful, so > I calculated the cosine content during this period using > g_analyze -f proj5ns.xvg -cc proj5ns_cc.xvg -b 3300 -e 3890 > and it gave: "Cosine content of set 1 with 0.5 periods: 0.297911" > > I want to know whether the essential dynamics is meaningful? The cosine > content of whole 5 ns is relative high, does it mean that the whole > trajectory is not meaningful? In another word, is it reasonable to use > "-b" and "-e" in the cosine content calculation? > What do you mean only a fraction is useful? First check for equilibration (energy, rmsd etc.) then do the ED sampling after that, for a period that is considerably longer than the equilibration, e.g. an order of magnitude. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -------------- next part -------------- An HTML attachment was scrubbed... URL: From yanmaocai at 126.com Mon Sep 11 03:40:40 2006 From: yanmaocai at 126.com (M. Yan) Date: Mon, 11 Sep 2006 09:40:40 +0800 (CST) Subject: [gmx-users] May I use "-b" and "- e" in the cosine con tent calculation of PC? In-Reply-To: <4504B9E1.7000408@xray.bmc.uu.se> References: <45037CD7.000033.15774@bj126app14.126.com> <4504970C.6040704@xray.bmc.uu.se> <4504AED1.000122.13981@bj126app26.126.com> <4504B9E1.7000408@xray.bmc.uu.se> Message-ID: <4504BE98.0000A4.14242@bj126app18.126.com> Thank you very much. The significant conformation changes occurred between 3.3ns and 3.9ns, which I am interested for. The cosine content in this 0.6ns is low (just 0.29; calculated by "g_analyze -f proj5ns.xvg -cc proj5ns_cc.xvg -b 3300 -e 3890"); I want to know whether it indicates that the movement of protein IN THIS 0.6ns is believable? -----Original Message----- From:"David van der Spoel" Sent:2006-09-11 09:20:33 To:"M. Yan" Title :Re: [gmx-users] May I use "-b" and "- e" in the cosine con tent calculation of PC? M. Yan wrote: > Hi, > In fact I simulated 30 nanoseconds, but I found the system reached > equilibrium at 4.4 ns (by analyzing RMSD, Energy and visualizing, > etc.) and did not change significantly in the last 25 ns. Thus I want to > do an essential dynamics for the first 5 ns. > I also calculated the covariance matrix for the whole 30 nanoseconds, > but the cosine content of PC1 is still as high as 0.710. However, MD > simulation longer than 30 ns is beyond our compute ability. Then what > shall I do? > > Thanks. > > > > Try ED of the last 25 ns only. The first 5 represent equilibration and unless you are specifically interested in th force field issues etc. related to that, you should discard those 5 ns for analysis. Then try to do other analyses as well and try to make sense of the whole simulation. IIRC the cosine content being high indicates that the protein performs a random walk on a relatively flat free energy surface. This is informative in itself but needs to be considered in the context of additional analysis and the background of your investigation. -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ -------------- next part -------------- An HTML attachment was scrubbed... URL: From spoel at xray.bmc.uu.se Mon Sep 11 04:31:34 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Sun, 10 Sep 2006 19:31:34 -0700 Subject: [gmx-users] May I use "-b" and "- e" in the cosine con tent calculation of PC? In-Reply-To: <4504BE98.0000A4.14242@bj126app18.126.com> References: <45037CD7.000033.15774@bj126app14.126.com> <4504970C.6040704@xray.bmc.uu.se> <4504AED1.000122.13981@bj126app26.126.com> <4504B9E1.7000408@xray.bmc.uu.se> <4504BE98.0000A4.14242@bj126app18.126.com> Message-ID: <4504CA86.5050709@xray.bmc.uu.se> M. Yan wrote: > Thank you very much. > > The significant conformation changes occurred between 3.3ns and 3.9ns, > which I am interested for. The cosine content in this 0.6ns is low (just > 0.29; calculated by "g_analyze -f proj5ns.xvg -cc proj5ns_cc.xvg -b 3300 > -e 3890"); I want to know whether it indicates that the movement of > protein IN THIS 0.6ns is believable? > > That depends, since you only see a single event in your 30 ns. It would be more convincing if you could show that this is reproducible, by doing multiple simulations with different conditions (e.g. velocities, temperature, starting structure). If it then happens early on in the simulations, and they all converge to the same structure as your 30 ns simulation, then it would be convincing... -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From d.s.mueller at rug.nl Mon Sep 11 05:39:43 2006 From: d.s.mueller at rug.nl (Daniela S. Mueller) Date: Mon, 11 Sep 2006 13:39:43 +1000 Subject: [gmx-users] problem with dimer simulation ! In-Reply-To: References: <000c01c6d3ef$aca225f0$e5fd89dd@mychat44e50e4f> Message-ID: <4504DA7F.6000406@rug.nl> hi cw, using trjconv -pbc nojump should remove the jumps. then you can analyse interactions between different chains, while it doesn't matter for the analysis where they diffuse. daniela Kay Gottschalk wrote: > try - cluster, and then as cluster group protein. > Kay. > > On Sep 9, 2006, at 11:09 AM, C.W. Liang wrote: > >> hi, all user: >> >> i performed the dimer simulation, and want to realize the interaction >> between two peptides. >> but frequently, i encountered this kind of problem: sometimes >> peptides moved out of the box, and sometimes they jumped back. >> i have tried so many way to pull them back with trjconv command, but >> still cause some unexpected problem. >> for example, peptides break to many parts ( with -pbc whole ) >> or diffuse out of box gradually ( with -pbc nojump ) >> with -ur or -center still not the trajectory i really want. i >> think maybe there are some tricks to perform. >> any suggestions for me ? thanks sooooooooooo much! -- Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland. -- Daniela S. Mueller Biologist (Dipl. Biol.) ______________________________________________________________________ - Molecular Dynamics Group, UQ - Address: School of Molecular and Microbial Sciences (SMMS) Chemistry Building (#68) University of Queensland Qld 4072, Brisbane Australia Phone: +61-7-33653732 Website: http://ilc00f.facbacs.uq.edu.au/SMMS/a_mark/Front.htm ********************************************************************** - MD group, RuG - Address: Molecular Dynamics Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands Website: http://www.rug.nl/gbb/md ______________________________________________________________________ From sunnytov at hotmail.com Mon Sep 11 06:38:42 2006 From: sunnytov at hotmail.com (=?ks_c_5601-1987?B?wMwgvLHB1g==?=) Date: Mon, 11 Sep 2006 13:38:42 +0900 Subject: [gmx-users] constrained minimization In-Reply-To: <20060911014119.B46872407E@xray.bmc.uu.se> Message-ID: Dear All I just saw from the mailing list that David answered that the restrained minimization can be done and it is different from the constrained minimization. For the torsional parameter optimization, I think I need to run minimization after constraining torsion angles. Does anyone know the way to constrain the torsion angle during minimization? Thank you in advance Sunjoo From alokjain at iitk.ac.in Mon Sep 11 11:04:36 2006 From: alokjain at iitk.ac.in (alokjain at iitk.ac.in) Date: Mon, 11 Sep 2006 14:34:36 +0530 (IST) Subject: [gmx-users] Dihedral angle in OPLS-AA force field In-Reply-To: <2098.150.101.115.79.1157759472.squirrel@sqmail.anu.edu.au> References: <1ea820a30609081026o7fe5f43bsfa010f91afa1f432@mail.gmail.com> <2098.150.101.115.79.1157759472.squirrel@sqmail.anu.edu.au> Message-ID: <2222.172.26.116.101.1157965476.squirrel@newwebmail.iitk.ac.in> Dear All, I have a basic question on Dihedral angle in OPLS-AA force field. I read some of the papers related to development of OPLS force field where they have different formula for calculating the torsion angle I think that is Ryckaert-Bellemans function, but there is no separate term for Improper dihedral term. when I tried to run a simulation using OPLS-AA force field gromacs 3.2.1 version (pdb2gmx option 3) I got following energy terms in my log file. Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 1.15231e+03 2.92374e+03 1.73760e+02 1.32334e+03 1.86599e+03 Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR) 5.03326e+03 1.39004e+05 -1.66722e+03 -9.54632e+05 -5.37046e+04 Potential Kinetic En. Total Energy Temperature Pressure (bar) -8.58528e+05 1.57277e+05 -7.01250e+05 3.04174e+02 -4.80269e+01 so I am getting two proper dihedral term in output(Proper Dih. and Ryckaert-Bell.).But when I checked the ffoplsaabon.itp file I got following comments Improper OPLS dihedrals to keep groups planar. ; (OPLS doesnt use improper for chiral atoms). ; Since these functions are periodic of the form 1-cos(2*x), the are ; actually implemented as proper dihedrals [1+cos(2*x+180)] for the moment, ; to keep things compatible. So its mean Proper Dih. which I am getting, In reality it is Improper Dihedral? and Ryckaert-Bell for proper dihedral, (please correct me if I am wrong).But in original OPLS force field Improper Dihedral was not defined so how we can justify uses of Improper Dihedral. Best regards, Alok From tsjerkw at gmail.com Mon Sep 11 11:32:05 2006 From: tsjerkw at gmail.com (Tsjerk Wassenaar) Date: Mon, 11 Sep 2006 11:32:05 +0200 Subject: [gmx-users] Gromacs version In-Reply-To: References: <20060909071327.81463.qmail@web8906.mail.in.yahoo.com> Message-ID: <8ff898150609110232g26b2e524pb96a09edee293021@mail.gmail.com> Hi Raghu, First of all, if all conditions are equal the two simulations should be drawn from the same ensemble and should for that reason be "comparable". However, some routines have changed and we don't really know whether and how this might influence the ensemble. The best way to check is to compare simulations. But for that you either need full convergence or need to have more than one simulation run with each force field (keeping all other conditions equal). Best, Tsjerk On 9/9/06, Chenyue Xing wrote: > I think the statistical reserves but the two trajectories are not exactly > the same. > > > > On 9/9/06, Ragothaman Yennamalli wrote: > > Dear all, > > I have a query, > > 1. Are two trajectories comparable if each one of them > > has been run in a different version of gromacs? Eg, > > v3.2 and v3.3. > > > > Thanks in advance, > > Regards, > > Raghu > > > > ************************************** > > Y. M. Ragothaman, > > Research Scholar, > > Centre for Computational Biology and Bioinformatics, > > School of Information Technology, > > Jawaharlal Nehru University, > > New Delhi - 110067. > > > > Telephone: 91-11-26717568, 26717585 > > Facsimile: 91-11-26717586 > > ************************************** > > > > > > > > > __________________________________________________________ > > Yahoo! India Answers: Share what you know. Learn something new > > http://in.answers.yahoo.com/ > > _______________________________________________ > > gmx-users mailing list gmx-users at gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-request at gromacs.org. > > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > > > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 From kwichapong at gmail.com Mon Sep 11 11:59:24 2006 From: kwichapong at gmail.com (kanin wichapong) Date: Mon, 11 Sep 2006 11:59:24 +0200 Subject: [gmx-users] constraint distance Message-ID: <172bb8a80609110259r5551643dw4f1fc999c68963c7@mail.gmail.com> Dear All I would like to know how to constraint the distance between the different molecule, ex. the ligand and the protein. As far as I know whatever to do the constraint, distance, angle dihedral, it can do just in the same molecule. Thank you in advance for all of your help. With Best all regard, Kanin -------------- next part -------------- An HTML attachment was scrubbed... URL: From tsjerkw at gmail.com Mon Sep 11 12:17:16 2006 From: tsjerkw at gmail.com (Tsjerk Wassenaar) Date: Mon, 11 Sep 2006 12:17:16 +0200 Subject: [gmx-users] May I use "-b" and "- e" in the cosine con tent calculation of PC? In-Reply-To: <4504CA86.5050709@xray.bmc.uu.se> References: <45037CD7.000033.15774@bj126app14.126.com> <4504970C.6040704@xray.bmc.uu.se> <4504AED1.000122.13981@bj126app26.126.com> <4504B9E1.7000408@xray.bmc.uu.se> <4504BE98.0000A4.14242@bj126app18.126.com> <4504CA86.5050709@xray.bmc.uu.se> Message-ID: <8ff898150609110317i25d72cb9gb677ca136444d700@mail.gmail.com> Hi Mao-Cai Yan, A high cosine content usually means you're not in equilibrium, or your trajectory includes the part in which the system is going to equilibrium. Now, apparently, you're not interested in equilibrium, but rather in some event of change, which may be required to go from the starting structure to the equilibrium state or may be a common transition in equilibrium (in which case you should definitely observe it more often before claiming anything regarding equilibrium). A high cosine content in itself is not a qualitative check for your simulation or fof the principal components extracted from it. It merely indicates that you're looking at an event of change of your system, which can be the relaxation from the starting structure or an undersampled transition, common to your equilibrium state. To say anything about equilibrium it would also be better to look at the RMSD from the time averaged structure obtained at the end of the simulation, which is a much better indicator than the RMSD from the starting structure. Note that the number of possible conformations increases rapidly with increasing RMSD, and you'll find the RMSD level off well before you have true convergence. For larger systems this may take 15-25 ns or more! Hope it helps, Tsjerk On 9/11/06, David van der Spoel wrote: > M. Yan wrote: > > Thank you very much. > > > > The significant conformation changes occurred between 3.3ns and 3.9ns, > > which I am interested for. The cosine content in this 0.6ns is low (just > > 0.29; calculated by "g_analyze -f proj5ns.xvg -cc proj5ns_cc.xvg -b 3300 > > -e 3890"); I want to know whether it indicates that the movement of > > protein IN THIS 0.6ns is believable? > > > > > That depends, since you only see a single event in your 30 ns. It would > be more convincing if you could show that this is reproducible, by doing > multiple simulations with different conditions (e.g. velocities, > temperature, starting structure). If it then happens early on in the > simulations, and they all converge to the same structure as your 30 ns > simulation, then it would be convincing... > > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 From tsjerkw at gmail.com Mon Sep 11 12:19:46 2006 From: tsjerkw at gmail.com (Tsjerk Wassenaar) Date: Mon, 11 Sep 2006 12:19:46 +0200 Subject: [gmx-users] constraint distance In-Reply-To: <172bb8a80609110259r5551643dw4f1fc999c68963c7@mail.gmail.com> References: <172bb8a80609110259r5551643dw4f1fc999c68963c7@mail.gmail.com> Message-ID: <8ff898150609110319kb53bf41lffb4f9dd5fb0b1d2@mail.gmail.com> Hi Kanin, The only way to get away with that is to merge your two parts to form one molecule, with the only connection being a distance_restraint (or another bonded term if you want to emulate bond-like behaviour such as a salt-bridge). Best, Tsjerk On 9/11/06, kanin wichapong wrote: > Dear All > I would like to know how to constraint the distance between the > different molecule, ex. the ligand and the protein. As far as I know > whatever to do the constraint, distance, angle dihedral, it can do just in > the same molecule. > Thank you in advance for all of your help. > > With Best all regard, > Kanin > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 From petrucci86 at vip.sina.com Mon Sep 11 12:28:28 2006 From: petrucci86 at vip.sina.com (C.W. Liang) Date: Mon, 11 Sep 2006 18:28:28 +0800 Subject: [gmx-users] Re: problem with dimer simulation ! Message-ID: <001501c6d58d$07080930$e5fd89dd@mychat44e50e4f> try - cluster, and then as cluster group protein. Kay. hello, Kay thanks so much for your advice, but with -pbc cluster, one of the two peptides still move out of the box and frequently jump back. i have no idea about it, any else should i do ? best regards, Liang -------------- next part -------------- An HTML attachment was scrubbed... URL: From petrucci86 at vip.sina.com Mon Sep 11 12:36:22 2006 From: petrucci86 at vip.sina.com (C.W. Liang) Date: Mon, 11 Sep 2006 18:36:22 +0800 Subject: [gmx-users] Re: problem with dimer simulation ! Message-ID: <002101c6d58e$22466970$e5fd89dd@mychat44e50e4f> hi cw, using trjconv -pbc nojump should remove the jumps. then you can analyse interactions between different chains, while it doesn't matter for the analysis where they diffuse. daniela hello, daniela thanks for your reply, it really doesn't matter when i calculate the distance between two peptides ? best regards, Liang -------------- next part -------------- An HTML attachment was scrubbed... URL: From yanmaocai at 126.com Mon Sep 11 13:11:04 2006 From: yanmaocai at 126.com (M. Yan) Date: Mon, 11 Sep 2006 19:11:04 +0800 (CST) Subject: [gmx-users] May I use "-b" and "- e" in the cosine co n tent calculation of PC? Message-ID: <45054448.000090.23219@bj126app19.126.com> Thank you, Tsjerk & David. Judging from RMSD and other analysis, the system has been in well equilibrium at 5 ns; (however, the cosine contents of last 25 ns and whole 30 ns are also higher than 0.7.) The RMSD during the last 25 nanoseconds (compared to the conformation at 5ns) is within 0.25 nm. After read your letter, I think that the PC1 may be useful, but it cannot represent the global motion of the protein very well because it has not been sampled sufficiently; that is, the significant conformation change observed in PC1 may in fact occur BY ACCIDENT. Did I understand right? And do you think it will help if I perform multiple MD simulations to test the reproducibility, just as David suggested? (It is quite time-consuming.) Best regards. Mao-Cai Yan -----------Original Message----------------- Send: 2006-09-11 18:17:16 From: "Tsjerk Wassenaar" To:"Discussion list for GROMACS users" Subject: Re: [gmx-users] May I use "-b" and "- e" in the cosine con tent calculation of PC? Hi Mao-Cai Yan, A high cosine content usually means you're not in equilibrium, or your trajectory includes the part in which the system is going to equilibrium. Now, apparently, you're not interested in equilibrium, but rather in some event of change, which may be required to go from the starting structure to the equilibrium state or may be a common transition in equilibrium (in which case you should definitely observe it more often before claiming anything regarding equilibrium). A high cosine content in itself is not a qualitative check for your simulation or fof the principal components extracted from it. It merely indicates that you're looking at an event of change of your system, which can be the relaxation from the starting structure or an undersampled transition, common to your equilibrium state. To say anything about equilibrium it would also be better to look at the RMSD from the time averaged structure obtained at the end of the simulation, which is a much better indicator than the RMSD from the starting structure. Note that the number of possible conformations increases rapidly with increasing RMSD, and you'll find the RMSD level off well before you have true convergence. For larger systems this may take 15-25 ns or more! Hope it helps, Tsjerk On 9/11/06, David van der Spoel wrote: > M. Yan wrote: > > Thank you very much. > > > > The significant conformation changes occurred between 3.3ns and 3.9ns, > > which I am interested for. The cosine content in this 0.6ns is low (just > > 0.29; calculated by "g_analyze -f proj5ns.xvg -cc proj5ns_cc.xvg -b 3300
> > -e 3890"); I want to know whether it indicates that the movement of > > protein IN THIS 0.6ns is believable? > > > > > That depends, since you only see a single event in your 30 ns. It would > be more convincing if you could show that this is reproducible, by doing > multiple simulations with different conditions (e.g. velocities, > temperature, starting structure). If it then happens early on in the > simulations, and they all converge to the same structure as your 30 ns > simulation, then it would be convincing... > > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ -------------- next part -------------- An HTML attachment was scrubbed... URL: From spoel at xray.bmc.uu.se Mon Sep 11 14:05:58 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Mon, 11 Sep 2006 05:05:58 -0700 Subject: [gmx-users] constrained minimization In-Reply-To: References: Message-ID: <45055126.4060406@xray.bmc.uu.se> ? ?? wrote: > Dear All > > I just saw from the mailing list that David answered that the restrained > minimization can be done and it is different from the constrained > minimization. For the torsional parameter optimization, I think I need > to run minimization after constraining torsion angles. Does anyone know > the way to constrain the torsion angle during minimization? > this is not implemented I'm afraid. Do you have a reference describing how to do it? > Thank you in advance > Sunjoo > > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From una.bjarnadottir at ucd.ie Mon Sep 11 13:00:00 2006 From: una.bjarnadottir at ucd.ie (Una Bjarnadottir) Date: Mon, 11 Sep 2006 12:00:00 +0100 Subject: [gmx-users] genion causing atom to be in multiple T-Coupling groups Message-ID: <450541B0.50807@ucd.ie> Dear Users, I'm hoping for an answear on my problem with neutralizing my system adding 3 Cl ions with genion. When running grompp after genion with the new generated .gro file I get this error: Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1) which is the last water atom (total in system 33003) and groups 15 and 1 are Cl and protein groups if I on the other hand do not neutralize the system the run goes fine! When looking into the .ndx file atom 33000 is in 4 groups; 0 (system), 11 (non-protein), 14 (SOL) and 16 (other). How can I change the group definitions and make sure the groups do not overlap and to be unique? It seems to be something wrong with how the genion works for me. I followed the tutorial and chose the SOL group and water molecules were replaced by the Cl ions. Than I modifyed the .top file and took 3 sol molecules and added the 3 ions. Please help because have not been able to fix the problem with related letters on the subject on the list. Best regards, Una Bjarnadottir .top before: ; Include generic topology for ions #include "ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound #mols Protein_E 1 Protein_I 1 Protein_A 1 SOL 9719 .top after ; Include generic topology for ions #include "ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound #mols Protein_E 1 Protein_I 1 Protein_A 1 SOL 9716 CL- 3 These are my commands: # #Run grompp # emfile_mdpfile='em.mdp' emout='em_out.mdp' structure_file='em.tpr' os.system('/usr/local/bin/grompp -f '+emfile_mdpfile+ ' -po ' +emout+ ' -c ' +water_grofile+ ' -o ' +structure_file+ ' -p ' +topologyfile) # #Run genion # ion_out='ion.gro' os.system('/usr/local/bin/genion -s '+structure_file+ ' -o ' +ion_out+ ' -nname Cl -nn 3') # #Run grompp # structure_file_after_genion='em_genion.tpr' os.system('/usr/local/bin/grompp -f '+emfile_mdpfile+ ' -po ' +emout+ ' -c ' +ion_out+ ' -o ' +structure_file_after_genion+ ' -p ' +topologyfile) From spoel at xray.bmc.uu.se Mon Sep 11 14:22:22 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Mon, 11 Sep 2006 05:22:22 -0700 Subject: [gmx-users] genion causing atom to be in multiple T-Coupling groups In-Reply-To: <450541B0.50807@ucd.ie> References: <450541B0.50807@ucd.ie> Message-ID: <450554FE.2080808@xray.bmc.uu.se> Una Bjarnadottir wrote: > Dear Users, > > I'm hoping for an answear on my problem with neutralizing my system > adding 3 Cl ions with genion. When running grompp after genion with the > new generated .gro file I get this error: > > Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1) > > which is the last water atom (total in system 33003) and groups 15 and 1 > are Cl and protein groups if I on the other hand do not neutralize the > system the run goes fine! When looking into the .ndx file atom 33000 is > in 4 groups; 0 (system), 11 (non-protein), 14 (SOL) and 16 (other). > How can I change the group definitions and make sure the groups do not > overlap and to be unique? > It seems to be something wrong with how the genion works for me. I > followed the tutorial and chose the SOL group and water molecules were > replaced by the Cl ions. Than I modifyed the .top file and took 3 sol > molecules and added the 3 ions. > > Please help because have not been able to fix the problem with related > letters on the subject on the list. > > Best regards, Una Bjarnadottir > What do your tcoupl groups look like? Could it be System SOL? The number may be confusing, you should subtract one from them when compared to the output from gmxcheck -n index.ndx So it seems that atom 33000 (numbering in the coordinate file) is in groups 14 and 0. Maybe you should make a new index file after genion. Note that it is good practice to make the ions part of the solvent T coupling group. -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From blegbirk at yahoo.dk Mon Sep 11 14:26:58 2006 From: blegbirk at yahoo.dk (Soren Enemark) Date: Mon, 11 Sep 2006 14:26:58 +0200 (CEST) Subject: SV: Re: [gmx-users] constraint distance In-Reply-To: <8ff898150609110319kb53bf41lffb4f9dd5fb0b1d2@mail.gmail.com> Message-ID: <20060911122658.19571.qmail@web27410.mail.ukl.yahoo.com> Hi, maybe I am misunderstanding either the manual or the topic.. but - in my world - I never stop being puzzled by the part of chapt 6 in the manual which apparently says that such distance constraining is possible even though it (seems) to be secretly known that it is _not_ possible unless one uses the method suggested below. I believe, I suggest adding a comment in the manual. -Soren Tsjerk Wassenaar skrev: Hi Kanin, The only way to get away with that is to merge your two parts to form one molecule, with the only connection being a distance_restraint (or another bonded term if you want to emulate bond-like behaviour such as a salt-bridge). Best, Tsjerk On 9/11/06, kanin wichapong wrote: > Dear All > I would like to know how to constraint the distance between the > different molecule, ex. the ligand and the protein. As far as I know > whatever to do the constraint, distance, angle dihedral, it can do just in > the same molecule. > Thank you in advance for all of your help. > > With Best all regard, > Kanin > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -------------- next part -------------- An HTML attachment was scrubbed... URL: From spoel at xray.bmc.uu.se Mon Sep 11 14:43:38 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Mon, 11 Sep 2006 05:43:38 -0700 Subject: SV: Re: [gmx-users] constraint distance In-Reply-To: <20060911122658.19571.qmail@web27410.mail.ukl.yahoo.com> References: <20060911122658.19571.qmail@web27410.mail.ukl.yahoo.com> Message-ID: <450559FA.30900@xray.bmc.uu.se> Soren Enemark wrote: > Hi, > maybe I am misunderstanding either the manual or the topic.. but - in > my world - > I never stop being puzzled by the part of chapt 6 in the manual which > apparently > says that such distance constraining is possible even though it (seems) > to be > secretly known that it is _not_ possible unless one uses the method > suggested > below. > I believe, I suggest adding a comment in the manual. > can you be more specific which part of the manual you mean? > -Soren > > */Tsjerk Wassenaar /* skrev: > > Hi Kanin, > > The only way to get away with that is to merge your two parts to form > one molecule, with the only connection being a distance_restraint (or > another bonded term if you want to emulate bond-like behaviour such as > a salt-bridge). > > Best, > > Tsjerk > > On 9/11/06, kanin wichapong wrote: > > Dear All > > I would like to know how to constraint the distance between the > > different molecule, ex. the ligand and the protein. As far as I know > > whatever to do the constraint, distance, angle dihedral, it can > do just in > > the same molecule. > > Thank you in advance for all of your help. > > > > With Best all regard, > > Kanin > > > > _______________________________________________ > > gmx-users mailing list gmx-users at gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-request at gromacs.org. > > Can't post? Read > > http://www.gromacs.org/mailing_lists/users.php > > > > > > > -- > > Tsjerk A. Wassenaar, M.Sc. > Groningen Biomolecular Sciences and Biotechnology Institute (GBB) > Dept. of Biophysical Chemistry > University of Groningen > Nijenborgh 4 > 9747AG Groningen, The Netherlands > +31 50 363 4336 > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From spoel at xray.bmc.uu.se Mon Sep 11 14:52:10 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Mon, 11 Sep 2006 05:52:10 -0700 Subject: [gmx-users] Re: problem with dimer simulation ! In-Reply-To: <001501c6d58d$07080930$e5fd89dd@mychat44e50e4f> References: <001501c6d58d$07080930$e5fd89dd@mychat44e50e4f> Message-ID: <45055BFA.2070503@xray.bmc.uu.se> C.W. Liang wrote: > try - cluster, and then as cluster group protein. > Kay. > hello, Kay > > thanks so much for your advice, but with -pbc cluster, one of the two > peptides still move out of the box and frequently jump back. > i have no idea about it, any else should i do ? > merge the peptides into one protein (pdb2gmx -merge) and make a distance restraint between them with distance much larger than the actual distance. you only need to do this for post-processing the output, not for the simulation. > best regards, > > Liang > > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From mark.abraham at anu.edu.au Mon Sep 11 15:08:15 2006 From: mark.abraham at anu.edu.au (Mark Abraham) Date: Mon, 11 Sep 2006 23:08:15 +1000 (EST) Subject: SV: Re: [gmx-users] constraint distance In-Reply-To: <20060911122658.19571.qmail@web27410.mail.ukl.yahoo.com> References: <8ff898150609110319kb53bf41lffb4f9dd5fb0b1d2@mail.gmail.com> <20060911122658.19571.qmail@web27410.mail.ukl.yahoo.com> Message-ID: <60892.150.203.145.27.1157980095.squirrel@sqmail.anu.edu.au> > Hi, > maybe I am misunderstanding either the manual or the topic.. but - in my > world - > I never stop being puzzled by the part of chapt 6 in the manual which > apparently > says that such distance constraining is possible even though it (seems) > to be > secretly known that it is _not_ possible unless one uses the method > suggested > below. > I believe, I suggest adding a comment in the manual. I agree that a comment in the restrains section of Chapter 4 would be in order. The truth that you can only use restraints between atoms of the same molecule is clearly implied by Table 5.4, but that's a bit oblique. Mark From spoel at xray.bmc.uu.se Mon Sep 11 15:14:20 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Mon, 11 Sep 2006 06:14:20 -0700 Subject: [gmx-users] Dihedral angle in OPLS-AA force field In-Reply-To: <2222.172.26.116.101.1157965476.squirrel@newwebmail.iitk.ac.in> References: <1ea820a30609081026o7fe5f43bsfa010f91afa1f432@mail.gmail.com> <2098.150.101.115.79.1157759472.squirrel@sqmail.anu.edu.au> <2222.172.26.116.101.1157965476.squirrel@newwebmail.iitk.ac.in> Message-ID: <4505612C.3080803@xray.bmc.uu.se> alokjain at iitk.ac.in wrote: > Dear All, > > I have a basic question on Dihedral angle in OPLS-AA force field. > > I read some of the papers related to development of OPLS force field where > they have different formula for calculating the torsion angle > I think that is Ryckaert-Bellemans function, but there is no separate term > for Improper dihedral term. > > when I tried to run a simulation using OPLS-AA force field gromacs 3.2.1 > version (pdb2gmx option 3) I got following energy terms in my log file. > > Energies (kJ/mol) > Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 > 1.15231e+03 2.92374e+03 1.73760e+02 1.32334e+03 1.86599e+03 > Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR) > 5.03326e+03 1.39004e+05 -1.66722e+03 -9.54632e+05 -5.37046e+04 > Potential Kinetic En. Total Energy Temperature Pressure (bar) > -8.58528e+05 1.57277e+05 -7.01250e+05 3.04174e+02 -4.80269e+01 > > so I am getting two proper dihedral term in output(Proper Dih. and > Ryckaert-Bell.).But when I checked the ffoplsaabon.itp file I got > following comments > > Improper OPLS dihedrals to keep groups planar. > ; (OPLS doesnt use improper for chiral atoms). > ; Since these functions are periodic of the form 1-cos(2*x), the are > ; actually implemented as proper dihedrals [1+cos(2*x+180)] for the moment, > ; to keep things compatible. > > So its mean Proper Dih. which I am getting, In reality it is Improper > Dihedral? and Ryckaert-Bell for proper dihedral, (please correct me if > I am wrong).But in original OPLS force field Improper Dihedral was not > defined so how we can justify uses of Improper Dihedral. > yes that's correct. AFAIK improper dihedrals are used in OPLS for instance for keeping rings flat. -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From mark.abraham at anu.edu.au Mon Sep 11 15:14:10 2006 From: mark.abraham at anu.edu.au (Mark Abraham) Date: Mon, 11 Sep 2006 23:14:10 +1000 (EST) Subject: [gmx-users] genion causing atom to be in multiple T-Coupling groups In-Reply-To: <450541B0.50807@ucd.ie> References: <450541B0.50807@ucd.ie> Message-ID: <33086.150.203.145.27.1157980450.squirrel@sqmail.anu.edu.au> > Dear Users, > > I'm hoping for an answear on my problem with neutralizing my system adding > 3 Cl ions with genion. When > running grompp after genion with the new generated .gro file I get this error: > > Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1) Read closely - "T-Coupling group", not "group". You choose the T-Coupling groups from among those in the .ndx file (or from the default groups in its absence, as you're doing here) and specify them in the .mdp file. Thus you should look there first of all. You need to use a disjoint set of T-Coupling groups, so this error is consistent with not having done that. If you were using .ndx file (which you aren't), it might be possible your .ndx file doesn't correspond to your post-genion structure and something weird happens. I'd expect GROMACS woud die with a more helpful error in such a case though. Mark From spoel at xray.bmc.uu.se Mon Sep 11 15:14:33 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Mon, 11 Sep 2006 06:14:33 -0700 Subject: [gmx-users] Dihedral angle in OPLS-AA force field In-Reply-To: <2222.172.26.116.101.1157965476.squirrel@newwebmail.iitk.ac.in> References: <1ea820a30609081026o7fe5f43bsfa010f91afa1f432@mail.gmail.com> <2098.150.101.115.79.1157759472.squirrel@sqmail.anu.edu.au> <2222.172.26.116.101.1157965476.squirrel@newwebmail.iitk.ac.in> Message-ID: <45056139.9000509@xray.bmc.uu.se> alokjain at iitk.ac.in wrote: > Dear All, > > I have a basic question on Dihedral angle in OPLS-AA force field. > > I read some of the papers related to development of OPLS force field where > they have different formula for calculating the torsion angle > I think that is Ryckaert-Bellemans function, but there is no separate term > for Improper dihedral term. > > when I tried to run a simulation using OPLS-AA force field gromacs 3.2.1 > version (pdb2gmx option 3) I got following energy terms in my log file. > > Energies (kJ/mol) > Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 > 1.15231e+03 2.92374e+03 1.73760e+02 1.32334e+03 1.86599e+03 > Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR) > 5.03326e+03 1.39004e+05 -1.66722e+03 -9.54632e+05 -5.37046e+04 > Potential Kinetic En. Total Energy Temperature Pressure (bar) > -8.58528e+05 1.57277e+05 -7.01250e+05 3.04174e+02 -4.80269e+01 > > so I am getting two proper dihedral term in output(Proper Dih. and > Ryckaert-Bell.).But when I checked the ffoplsaabon.itp file I got > following comments > > Improper OPLS dihedrals to keep groups planar. > ; (OPLS doesnt use improper for chiral atoms). > ; Since these functions are periodic of the form 1-cos(2*x), the are > ; actually implemented as proper dihedrals [1+cos(2*x+180)] for the moment, > ; to keep things compatible. > > So its mean Proper Dih. which I am getting, In reality it is Improper > Dihedral? and Ryckaert-Bell for proper dihedral, (please correct me if > I am wrong).But in original OPLS force field Improper Dihedral was not > defined so how we can justify uses of Improper Dihedral. > yes that's correct. AFAIK proper dihedrals are used in OPLS for instance for keeping rings flat. -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From blegbirk at yahoo.dk Mon Sep 11 15:47:37 2006 From: blegbirk at yahoo.dk (Soren Enemark) Date: Mon, 11 Sep 2006 15:47:37 +0200 (CEST) Subject: SV: Re: SV: Re: [gmx-users] constraint distance In-Reply-To: <450559FA.30900@xray.bmc.uu.se> Message-ID: <20060911134737.81658.qmail@web27409.mail.ukl.yahoo.com> David van der Spoel skrev: Soren Enemark wrote: > Hi, > maybe I am misunderstanding either the manual or the topic.. but - in > my world - > I never stop being puzzled by the part of chapt 6 in the manual which > apparently > says that such distance constraining is possible even though it (seems) > to be > secretly known that it is _not_ possible unless one uses the method > suggested > below. > I believe, I suggest adding a comment in the manual. > can you be more specific which part of the manual you mean? Basically almost anywhere in chapter 6 from 6.1 to 6.25 included. I mean, pulling works between 2 different molecules, why is it then obvious that constraining doesn't? > -Soren > > */Tsjerk Wassenaar /* skrev: > > Hi Kanin, > > The only way to get away with that is to merge your two parts to form > one molecule, with the only connection being a distance_restraint (or > another bonded term if you want to emulate bond-like behaviour such as > a salt-bridge). > > Best, > > Tsjerk > > On 9/11/06, kanin wichapong wrote: > > Dear All > > I would like to know how to constraint the distance between the > > different molecule, ex. the ligand and the protein. As far as I know > > whatever to do the constraint, distance, angle dihedral, it can > do just in > > the same molecule. > > Thank you in advance for all of your help. > > > > With Best all regard, > > Kanin > > > > _______________________________________________ > > gmx-users mailing list gmx-users at gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-request at gromacs.org. > > Can't post? Read > > http://www.gromacs.org/mailing_lists/users.php > > > > > > > -- > > Tsjerk A. Wassenaar, M.Sc. > Groningen Biomolecular Sciences and Biotechnology Institute (GBB) > Dept. of Biophysical Chemistry > University of Groningen > Nijenborgh 4 > 9747AG Groningen, The Netherlands > +31 50 363 4336 > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -------------- next part -------------- An HTML attachment was scrubbed... URL: From una.bjarnadottir at ucd.ie Mon Sep 11 15:58:56 2006 From: una.bjarnadottir at ucd.ie (Una Bjarnadottir) Date: Mon, 11 Sep 2006 14:58:56 +0100 Subject: [gmx-users] Re: genion causing atom to be in multiple T-Coupling groups In-Reply-To: <20060911131005.D49BE2407C@xray.bmc.uu.se> References: <20060911131005.D49BE2407C@xray.bmc.uu.se> Message-ID: <45056BA0.3080808@ucd.ie> Una Bjarnadottir wrote: >> Dear Users, >> >> I'm hoping for an answear on my problem with neutralizing my system >> adding 3 Cl ions with genion. When running grompp after genion with the >> new generated .gro file I get this error: >> >> Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1) >> >> which is the last water atom (total in system 33003) and groups 15 and 1 >> are Cl and protein groups if I on the other hand do not neutralize the >> system the run goes fine! When looking into the .ndx file atom 33000 is >> in 4 groups; 0 (system), 11 (non-protein), 14 (SOL) and 16 (other). >> How can I change the group definitions and make sure the groups do not >> overlap and to be unique? >> It seems to be something wrong with how the genion works for me. I >> followed the tutorial and chose the SOL group and water molecules were >> replaced by the Cl ions. Than I modifyed the .top file and took 3 sol >> molecules and added the 3 ions. >> >> Please help because have not been able to fix the problem with related >> letters on the subject on the list. >> >> Best regards, Una Bjarnadottir >> > > >>What do your tcoupl groups look like? tc-grps':'Protein OTHER CL- ###where I have to call SOL: OTHER otherwise error >>Could it be System SOL? >>The number may be confusing, you should subtract one from them when >>compared to the output from gmxcheck -n index.ndx >>So it seems that atom 33000 (numbering in the coordinate file) is in >>groups 14 and 0. Maybe you should make a new index file after genion. >>Note that it is good practice to make the ions part of the solvent T >>coupling group. I made the indes file after running genion using the .gro output file from genion generating it. Also I thought you would have to subtract one and it was groups 14 and 0 instead of 15 and 1. How would I have the ions part of the solvent T coupling group? By modifying the .top file to [ molecules ] ; Compound #mols Protein_E 1 Protein_I 1 Protein_A 1 SOL+CL- 9719 and than the tc-grps in the .mdp file accordingly to that. How will I define SOL and CL- together, I tryed SOL+CL- and SOL-CL- but Fatal error: No such moleculetype SOL+CL- came for both. Best regards David for your reply, Una David. From JeffreyCopps at creighton.edu Mon Sep 11 15:52:37 2006 From: JeffreyCopps at creighton.edu (Copps, Jeffrey) Date: Mon, 11 Sep 2006 08:52:37 -0500 Subject: [gmx-users] RE: gmx-users Digest, Vol 29, Issue 23 References: <20060911014118.9A47E24080@xray.bmc.uu.se> Message-ID: Message: 6 Date: Sun, 10 Sep 2006 18:02:50 -0700 From: David van der Spoel Subject: Re: [gmx-users] TFE .gro files To: Discussion list for GROMACS users Message-ID: <4504B5BA.2050106 at xray.bmc.uu.se> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Copps, Jeffrey wrote: > > Hello all, > > Does anyone have TFE (trifluoroethanol) .gro files that they might > be willing to share? Or, barring that, can anyone tell me how to create > a solvent .gro file? > > Much thanks, > > Jeff Copps > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php how about the united atom one in the share/gromacs/top directory? otherwise, use prodrg followed by genconf and pressure coupled MD. -- David. Unfortunately, unless it's under some unintuitive filename, it's missing from my share/top directory. Jeff -------------- next part -------------- An HTML attachment was scrubbed... URL: From spoel at xray.bmc.uu.se Mon Sep 11 16:00:20 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Mon, 11 Sep 2006 07:00:20 -0700 Subject: [gmx-users] Re: genion causing atom to be in multiple T-Coupling groups In-Reply-To: <45056BA0.3080808@ucd.ie> References: <20060911131005.D49BE2407C@xray.bmc.uu.se> <45056BA0.3080808@ucd.ie> Message-ID: <45056BF4.3030402@xray.bmc.uu.se> Una Bjarnadottir wrote: > Una Bjarnadottir wrote: > >>> Dear Users, >>> >>> I'm hoping for an answear on my problem with neutralizing my system >>> adding 3 Cl ions with genion. When running grompp after genion with >>> the new generated .gro file I get this error: >>> >>> Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1) >>> >>> which is the last water atom (total in system 33003) and groups 15 >>> and 1 are Cl and protein groups if I on the other hand do not >>> neutralize the system the run goes fine! When looking into the .ndx >>> file atom 33000 is in 4 groups; 0 (system), 11 (non-protein), 14 >>> (SOL) and 16 (other). How can I change the group definitions and >>> make sure the groups do not overlap and to be unique? >>> It seems to be something wrong with how the genion works for me. I >>> followed the tutorial and chose the SOL group and water molecules >>> were replaced by the Cl ions. Than I modifyed the .top file and took >>> 3 sol molecules and added the 3 ions. >>> >>> Please help because have not been able to fix the problem with >>> related letters on the subject on the list. >>> >>> Best regards, Una Bjarnadottir >>> >> >> >>> What do your tcoupl groups look like? > > tc-grps':'Protein OTHER CL- ###where I have to call SOL: OTHER > otherwise error > >>> Could it be System SOL? > >>> The number may be confusing, you should subtract one from them when >>> compared to the output from gmxcheck -n index.ndx >>> So it seems that atom 33000 (numbering in the coordinate file) is in >>> groups 14 and 0. Maybe you should make a new index file after genion. >>> Note that it is good practice to make the ions part of the solvent T >>> coupling group. > > I made the indes file after running genion using the .gro output file > from genion generating it. Also I thought you would have to subtract > one and it was groups 14 and 0 instead of 15 and 1. How would I have > the ions part of the solvent T coupling group? By modifying the .top > file to [ molecules ] > ; Compound #mols > Protein_E 1 > Protein_I 1 > Protein_A 1 > SOL+CL- 9719 > > and than the tc-grps in the .mdp file accordingly to that. How will I > define SOL and CL- together, I tryed SOL+CL- and SOL-CL- but Fatal > error: No such moleculetype SOL+CL- came for both. > Best regards David for your reply, Una David. in make_ndx you type 14 | 15 that will give you the combination of the two groups (if 14 is SOL and 15 is CL-) > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From spoel at xray.bmc.uu.se Mon Sep 11 16:04:22 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Mon, 11 Sep 2006 07:04:22 -0700 Subject: [gmx-users] RE: gmx-users Digest, Vol 29, Issue 23 In-Reply-To: References: <20060911014118.9A47E24080@xray.bmc.uu.se> Message-ID: <45056CE6.4090000@xray.bmc.uu.se> Copps, Jeffrey wrote: > > Message: 6 > Date: Sun, 10 Sep 2006 18:02:50 -0700 > From: David van der Spoel > Subject: Re: [gmx-users] TFE .gro files > To: Discussion list for GROMACS users > Message-ID: <4504B5BA.2050106 at xray.bmc.uu.se> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Copps, Jeffrey wrote: > > > > Hello all, > > > > Does anyone have TFE (trifluoroethanol) .gro files that they might > > be willing to share? Or, barring that, can anyone tell me how to create > > a solvent .gro file? > > > > Much thanks, > > > > Jeff Copps > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users mailing list gmx-users at gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-request at gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > how about the united atom one in the share/gromacs/top directory? > otherwise, use prodrg followed by genconf and pressure coupled MD. > > -- > David. > > Unfortunately, unless it's under some unintuitive filename, it's missing > from my share/top directory. > sorry can't find it anymore.. then you'll have to go the second route. > Jeff > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From jellby at yahoo.com Mon Sep 11 16:18:01 2006 From: jellby at yahoo.com (=?iso-8859-1?q?Ignacio=20Fern=E1ndez=20Galv=E1n?=) Date: Mon, 11 Sep 2006 15:18:01 +0100 (BST) Subject: [gmx-users] Free energy, frozen atoms and exclusions Message-ID: <20060911141801.97133.qmail@web33010.mail.mud.yahoo.com> Hi all, I'm trying to calculate solvation free energies and I've found something "strange". The thing is I'm interested in free energy of rigid molecules (I consider other contributions separately), typically a small solute molecule in water. I'm making a test with methanol. The setup is a frozen methanol molecule in a box of of water molecules. Since I'm considering rigid molecules, I create an .itp file with no bonded terms, just atoms (with charges and LJ). The methanol molecule is called MOH, and I have this in the .mdp: energy_grps = MOH energygrp_excl = MOH MOH freezegrps = MOH freezedim = y y y which should freeze the methanol and disregard all nonbonded terms between the methanol atoms (and there are no bonded terms). Well, after the usual equilibration and such, I get this output for the initial configuration with lambda=1: LJ (SR): 5.70341e+03 Coulomb (SR): -3.65377e+04 ... dVpot/dlambda: 2.81161e+02 It seems right, but after simulation for several lambda values I get a free energy of around 10 times what I would expect. Now I repeat exactly the same simulation, but adding all pairs of methanol atoms in the [exclusions] of the .itp file. For the same initial configuration as before, I get this: LJ (SR): 5.70341e+03 Coulomb (SR): -3.65377e+04 ... dVpot/dlambda: 2.14385e+00 (the only difference is in dVpot/dlambda). This (if I extrapolate) would give a much more sensible value for the free energy. As far as I could understand, having "energygrp_excl = MOH MOH" should be the same as putting all atoms in the [exclusions] section, but it obviously isn't, at least when it comes to calculating dVpot/dlambda. Is there something I'm missing? A bug/feature in the code? A limitation? Thanks in advance PS. As a side question, I'd say that, if I have a frozen molecule it would be best *not* to remove the center of mass motion (not even of the rest of the system). Am I right? ___________________________________________________________ Try the all-new Yahoo! Mail. "The New Version is radically easier to use" ? The Wall Street Journal http://uk.docs.yahoo.com/nowyoucan.html From gmx3 at hotmail.com Mon Sep 11 16:54:44 2006 From: gmx3 at hotmail.com (Berk Hess) Date: Mon, 11 Sep 2006 16:54:44 +0200 Subject: [gmx-users] Free energy, frozen atoms and exclusions In-Reply-To: <20060911141801.97133.qmail@web33010.mail.mud.yahoo.com> Message-ID: >From: Ignacio Fern?ndez Galv?n >Reply-To: Discussion list for GROMACS users >To: gmx-users at gromacs.org >Subject: [gmx-users] Free energy, frozen atoms and exclusions >Date: Mon, 11 Sep 2006 15:18:01 +0100 (BST) > >Hi all, > >I'm trying to calculate solvation free energies and I've found >something "strange". > >The thing is I'm interested in free energy of rigid molecules (I >consider other contributions separately), typically a small solute >molecule in water. I'm making a test with methanol. The setup is a >frozen methanol molecule in a box of of water molecules. Since I'm >considering rigid molecules, I create an .itp file with no bonded >terms, just atoms (with charges and LJ). The methanol molecule is >called MOH, and I have this in the .mdp: > >energy_grps = MOH >energygrp_excl = MOH MOH >freezegrps = MOH >freezedim = y y y > >which should freeze the methanol and disregard all nonbonded terms >between the methanol atoms (and there are no bonded terms). > >Well, after the usual equilibration and such, I get this output for the >initial configuration with lambda=1: > >LJ (SR): 5.70341e+03 >Coulomb (SR): -3.65377e+04 >... >dVpot/dlambda: 2.81161e+02 > >It seems right, but after simulation for several lambda values I get a >free energy of around 10 times what I would expect. > >Now I repeat exactly the same simulation, but adding all pairs of >methanol atoms in the [exclusions] of the .itp file. For the same >initial configuration as before, I get this: > >LJ (SR): 5.70341e+03 >Coulomb (SR): -3.65377e+04 >... >dVpot/dlambda: 2.14385e+00 > >(the only difference is in dVpot/dlambda). This (if I extrapolate) >would give a much more sensible value for the free energy. > >As far as I could understand, having "energygrp_excl = MOH MOH" should >be the same as putting all atoms in the [exclusions] section, but it >obviously isn't, at least when it comes to calculating dVpot/dlambda. > >Is there something I'm missing? A bug/feature in the code? A >limitation? If you are using PME, the mesh contribution is not excluded when using energygrp_excl, grompp should give you a warning about this. Adding all the pairs as exclusions solves this problem. > >Thanks in advance > >PS. As a side question, I'd say that, if I have a frozen molecule it >would be best *not* to remove the center of mass motion (not even of >the rest of the system). Am I right? Yes. Note that there are still issues with freeze-groups and pressure scaling as the rest of the system scales around your frozen atoms. There is currently no solution for this, although slow coupling would help. But why do you want to freeze the methonal? Things would be much easier with a free methanol. Berk. From jellby at yahoo.com Mon Sep 11 17:14:24 2006 From: jellby at yahoo.com (=?iso-8859-1?q?Ignacio=20Fern=E1ndez=20Galv=E1n?=) Date: Mon, 11 Sep 2006 16:14:24 +0100 (BST) Subject: [gmx-users] Free energy, frozen atoms and exclusions In-Reply-To: Message-ID: <20060911151424.16705.qmail@web33005.mail.mud.yahoo.com> --- Berk Hess wrote: > >Is there something I'm missing? A bug/feature in the code? A > >limitation? > > If you are using PME, the mesh contribution is not excluded when > using energygrp_excl, grompp should give you a warning about this. > Adding all the pairs as exclusions solves this problem. Thanks. Would that account for such a large difference, considering it's a neutral molecule (and at lambda=1, with no partial charges)? Well... since it's the derivative, and that means the free energy change from lambda=0 to lambda=1... yes that could be it. Is this mentioned in the manual? 'Cause I read about the [exclusions] section and it gives the advice to use energygrp_excl, but doesn't warn about this. Would normal Ewald or reaction field work as (I) expected? I guess I will keep using PME anyway, if it's as easy as adding the [exclusions]. > But why do you want to freeze the methonal? > Things would be much easier with a free methanol. At the moment this is only a test. I need the method to work for arbitrary molecules for which there are no force field parameters, only LJ. The atomic charges and intramolecular contributions I get them from other QM/MM calculations. I also need to compare with other rigid-body simulations. I'm not saying this is the best way to calculate free energies, but it's the way I need now :) Thanks a lot for the reply! PS. The manual mentions using "no" for "comm_mode", but grompp prefers "none" instead. ___________________________________________________________ All New Yahoo! Mail ? Tired of Vi at gr@! come-ons? Let our SpamGuard protect you. http://uk.docs.yahoo.com/nowyoucan.html From kwichapong at gmail.com Mon Sep 11 17:36:32 2006 From: kwichapong at gmail.com (kanin wichapong) Date: Mon, 11 Sep 2006 17:36:32 +0200 Subject: [gmx-users] constraint distance between ligand and protein Message-ID: <172bb8a80609110836w2beb8e67s8105e3982311c2b3@mail.gmail.com> Hi All, I would like to know how to make a distance constraint between the ligand and the protein. If I just merge two chain together by pdb2gmx, it can done if the two chain are both protein. However, if it is a ligand and protein, i can't merge together because there is no libraly for the ligand force field and then it can't generate the .itp or .top file Best Regard Kanin -------------- next part -------------- An HTML attachment was scrubbed... URL: From robertjo at physics.upenn.edu Mon Sep 11 16:54:21 2006 From: robertjo at physics.upenn.edu (Bob Johnson) Date: Mon, 11 Sep 2006 10:54:21 -0400 Subject: [gmx-users] File input/output error: Can not determine precision of trn file Message-ID: <1157986461.4505789d182ba@webmail.sas.upenn.edu> Hello everyone, It seems that one of my trajectory files has an error. I get the following message when using trjconv -f trajectory.trr. File input/output error: Can not determine precision of trn file I noticed that there was a previous question about this error message. However, the only available workaround pertained to trajectories saved in xtc format. Has there be any new developments for the trr format? Thanks, Bob From sunnytov at hotmail.com Mon Sep 11 18:44:52 2006 From: sunnytov at hotmail.com (=?ks_c_5601-1987?B?wMwgvLHB1g==?=) Date: Tue, 12 Sep 2006 01:44:52 +0900 Subject: [gmx-users] Re: constrained minimization (David van der Spoel) In-Reply-To: <20060911131004.A5B342407E@xray.bmc.uu.se> Message-ID: > > Dear All > > > > I just saw from the mailing list that David answered that the restrained > > minimization can be done and it is different from the constrained > > minimization. For the torsional parameter optimization, I think I need > > to run minimization after constraining torsion angles. Does anyone know > > the way to constrain the torsion angle during minimization? > > >this is not implemented I'm afraid. Do you have a reference describing >how to do it? > I am afraid not... From alokjain at iitk.ac.in Mon Sep 11 20:00:44 2006 From: alokjain at iitk.ac.in (alokjain at iitk.ac.in) Date: Mon, 11 Sep 2006 23:30:44 +0530 (IST) Subject: [gmx-users] OPLS-AA force field again regarding 1-4 interaction In-Reply-To: <45056139.9000509@xray.bmc.uu.se> References: <1ea820a30609081026o7fe5f43bsfa010f91afa1f432@mail.gmail.com> <2098.150.101.115.79.1157759472.squirrel@sqmail.anu.edu.au> <2222.172.26.116.101.1157965476.squirrel@newwebmail.iitk.ac.in> <45056139.9000509@xray.bmc.uu.se> Message-ID: <2082.172.26.116.101.1157997644.squirrel@newwebmail.iitk.ac.in> Thanks David for your reply, I have a another doubt on OPLS force field regarding 1-4 interaction. In manual (chapter 4 page no 62) it was written The use of RB potential implies exclusion of LJ interaction between first and the last atom of the dihedral (mean 1-4 interaction).So why I am getting LJ-14 and Coulomb-14 energy in my log file (see below) is there is any problem in this simulation or it is normal? Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 1.15231e+03 2.92374e+03 1.73760e+02 1.32334e+03 1.86599e+03 Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR) 5.03326e+03 1.39004e+05 -1.66722e+03 -9.54632e+05 -5.37046e+04 Potential Kinetic En. Total Energy Temperature Pressure (bar) -8.58528e+05 1.57277e+05 -7.01250e+05 3.04174e+02 -4.80269e+01 and what I understood from articles on OPLS force field that it scale down the LJ-14 and Coulomb-14 energy my a factor of two? as it is specify in ffoplsaa.itp file ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 3 yes 0.5 0.5 what about GROMOS96 force field, it is mention in manual (Chapter 4 page no 75) it also scale down the LJ-14 repulsion term . what I understood by manual that It uses separate parameter for LJ-14 interaction Is it is correct? If yes then It uses separate parameters only for LJ repulsive term or all the non bonded terms i.e. LJ repulsive,LJ attractive and for coulomb term? Best regards, Alok > alokjain at iitk.ac.in wrote: >> Dear All, >> >> I have a basic question on Dihedral angle in OPLS-AA force field. >> >> I read some of the papers related to development of OPLS force field >> where >> they have different formula for calculating the torsion angle >> I think that is Ryckaert-Bellemans function, but there is no separate >> term >> for Improper dihedral term. >> >> when I tried to run a simulation using OPLS-AA force field gromacs 3.2.1 >> version (pdb2gmx option 3) I got following energy terms in my log file. >> >> Energies (kJ/mol) >> Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 >> 1.15231e+03 2.92374e+03 1.73760e+02 1.32334e+03 1.86599e+03 >> Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR) >> 5.03326e+03 1.39004e+05 -1.66722e+03 -9.54632e+05 -5.37046e+04 >> Potential Kinetic En. Total Energy Temperature Pressure >> (bar) >> -8.58528e+05 1.57277e+05 -7.01250e+05 3.04174e+02 -4.80269e+01 >> >> so I am getting two proper dihedral term in output(Proper Dih. and >> Ryckaert-Bell.).But when I checked the ffoplsaabon.itp file I got >> following comments >> >> Improper OPLS dihedrals to keep groups planar. >> ; (OPLS doesnt use improper for chiral atoms). >> ; Since these functions are periodic of the form 1-cos(2*x), the are >> ; actually implemented as proper dihedrals [1+cos(2*x+180)] for the >> moment, >> ; to keep things compatible. >> >> So its mean Proper Dih. which I am getting, In reality it is Improper >> Dihedral? and Ryckaert-Bell for proper dihedral, (please correct me if >> I am wrong).But in original OPLS force field Improper Dihedral was not >> defined so how we can justify uses of Improper Dihedral. >> > > yes that's correct. AFAIK proper dihedrals are used in OPLS for instance > for keeping rings flat. > > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > From p.biswas at csuohio.edu Mon Sep 11 22:19:26 2006 From: p.biswas at csuohio.edu (Pradip Kumar Biswas) Date: Mon, 11 Sep 2006 16:19:26 -0400 Subject: [gmx-users] Re: Gromacs-CPMD: QMMM In-Reply-To: <34289.10.128.10.17.1158004344.squirrel@10.128.10.17> References: <34289.10.128.10.17.1158004344.squirrel@10.128.10.17> Message-ID: <3c40b1d1ff9e4adc77db3d976a2c34a9@csuohio.edu> Hi Amit, Please open epot.inc in SOURCE folder of CPMD-3.11.1, search for MAXNEAR and change the statement: PARAMETER (MAXNEAR=2000) to PARAMETER (MAXNEAR=5000) best, pb. On Sep 11, 2006, at 3:52 PM, amit at mbu.iisc.ernet.in wrote: > Dear Dr. Biswas, > I am getting following error while running gromacs-cpmd interface for > my > system. > > LMAX-OF-MMQ-EXP 0 > INTML-UPD-FREQ 10 > OUTRL-UPD-FREQ 50 > MM-Near 4289 > INTERFACE| Error: MAXNEAR not big enough! > Increase this value in epot.inc > > > PROGRAM STOPS IN SUBROUTINE INTERFACE| To many near atoms. [PROC= 0] > > > with regards, > amit > > -- Pradip K. Biswas, PhD. Research Associate, Department of Chemistry; Cleveland State University, Ohio-44115 Phone: 1-216-875-9723 http://comppsi.csuohio.edu/groups/people/biswas.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 852 bytes Desc: not available URL: From jmiranda at explicacoes.com Mon Sep 11 23:56:46 2006 From: jmiranda at explicacoes.com (JMiranda) Date: Mon, 11 Sep 2006 22:56:46 +0100 Subject: [gmx-users] unsubscribe In-Reply-To: <1157679961.4500cb59b996b@webmail.utoronto.ca> Message-ID: <00e501c6d5ed$32821870$0132a8c0@Paulo> gmx-users-request at gromacs.org -----Original Message----- From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of chris.neale at utoronto.ca Sent: sexta-feira, 8 de Setembro de 2006 2:46 To: gmx-users at gromacs.org Subject: [gmx-users] Re: Simulation problem with extended membrane system! Having actually looked back at my notes, here is what I did to extend pope.pdb into a larger system. However, the suggestion that I posted last time should work just as well. 1. Remove all waters 2. Duplicate the box until your heart's content. Make it larger than you actually want because the box will collapse to some extent. 3. MD with Z-only posre on lipid head groups (X and Y force components = zero). This step must be done with constant pressure (In this procedure, make sure to use isotropic pressure coupling so that the box max and min z don't come into contact with the membrane). NOTE for step 3: It is assumed that your edges line up with each other. Load the system into vmd and show periodic unit cells to make sure. If they line up poorly then I would find a new starting PDB. However, pope.pdb lines up well. 4. Adjust the z-dimension to what you want it to be, center your membrane in the z if you want to. 5. solvate the system. 6. Remove any waters that were placed within the membrane 7. energy minimize 8. posre run as before to allow the water to adjust to the membrane surfaces. However, during this run (and all the rest of the steps) I use semiisotropic Pcoupling. 9. equilibration phase without any position restraints 10. production run. If you are going to add protein, you could do that with the results of step 4 since most procedures involve stripping out any waters anyway. Again, the procedure that I outlined previously should work, but I have not tested that procedure, only this one. _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php From chris.neale at utoronto.ca Tue Sep 12 01:11:19 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Mon, 11 Sep 2006 19:11:19 -0400 Subject: [gmx-users] Re: Simulation problem with extended membrane system! Message-ID: <1158016279.4505ed1707ba6@webmail.utoronto.ca> I just remembered that I previously posted a script to assist in removing waters based on their z position: http://www.gromacs.org/pipermail/gmx-users/2006-May/021526.html >Back to the previous question, after solvate the lipids in water, can I >remove the water placed in the membrane with excel instead of script? Cause >with editconf we can know the z dimension of the lipids_only system, let's >say 6, so if I center the whole system with 0 0 0, the water molecules with >z coordinates below 3 and above -3 will be excluded. If I'm right, I think >excel can do it too, or the scripts have some advantages? From clarkzhy at tom.com Tue Sep 12 02:22:26 2006 From: clarkzhy at tom.com (=?gb2312?B?Y2xhcms=?=) Date: Tue, 12 Sep 2006 08:22:26 +0800 (CST) Subject: [gmx-users] problem about "order parameter" Message-ID: <4505FDC2.00008C.00743@bjapp34> I am performing some simulation about common protein.I am puzzled when I want to get the order parameter(S2, N-H bond in main chian) to compare with the result of my NMR experiment. Who can give me a detailed way to get this parameter in Gromacs3.3.1? Thanks ! -------------- next part -------------- An HTML attachment was scrubbed... URL: From spoel at xray.bmc.uu.se Tue Sep 12 02:59:26 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Mon, 11 Sep 2006 17:59:26 -0700 Subject: [gmx-users] problem about "order parameter" In-Reply-To: <4505FDC2.00008C.00743@bjapp34> References: <4505FDC2.00008C.00743@bjapp34> Message-ID: <4506066E.5030700@xray.bmc.uu.se> clark wrote: > I am performing some simulation about common protein.I am puzzled when I > want to get the order parameter(S2, N-H bond in main chian) to compare > with the result of my NMR experiment. > > Who can give me a detailed way to get this parameter in Gromacs3.3.1? > > Thanks ! > > g_rotacf you need very long simulations for this to converge. -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From wurl04 at iccas.ac.cn Tue Sep 12 05:35:33 2006 From: wurl04 at iccas.ac.cn (Rongliang Wu) Date: Tue, 12 Sep 2006 11:35:33 +0800 Subject: [gmx-users] changing the parameter numbers for torsion Message-ID: <20060912034209.419DD3E5@colibri.its.uu.se> hello,gmx-users i have a force field that contain 7 rychaert-bellemans dihedral coefficients, but in gromacs there are only 6, how can i manage it ? and where i should change the source code? regards! thanks! ????????Rongliang Wu ????????wurl04 at iccas.ac.cn ??????????2006-09-12 From spoel at xray.bmc.uu.se Tue Sep 12 05:44:07 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Mon, 11 Sep 2006 20:44:07 -0700 Subject: [gmx-users] changing the parameter numbers for torsion In-Reply-To: <20060912034209.419DD3E5@colibri.its.uu.se> References: <20060912034209.419DD3E5@colibri.its.uu.se> Message-ID: <45062D07.7060005@xray.bmc.uu.se> Rongliang Wu wrote: > hello,gmx-users > > i have a force field that contain 7 rychaert-bellemans dihedral coefficients, but in gromacs there are only 6, how can i manage it ? > and where i should change the source code? > maybe you can combine a RB with a proper dihedral with n=7 over the same bond. > regards! > > thanks! > > > ????????Rongliang Wu > ????????wurl04 at iccas.ac.cn > ??????????2006-09-12 > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chris.neale at utoronto.ca Tue Sep 12 07:33:53 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Tue, 12 Sep 2006 01:33:53 -0400 Subject: [gmx-users] re: non-bonded interactions in GROMACS Message-ID: <1158039233.450646c1b2442@webmail.utoronto.ca> >In manual (chapter 4 page no 62) it was written The use of RB potential >implies exclusion of LJ interaction between first and the last atom of the >dihedral (mean 1-4 interaction).So why I am getting LJ-14 and Coulomb-14 >energy in my log file (see below) is there is any problem in this >simulation or it is normal? Only the 1-4 interactions spanning RB potentials should be excluded from LJ-14 and coulomb-14. For example, lipid headgroups may be treated without RB's and the acyl chains treated with RB's. If you want to see where things are coming from, make an index file and then use enerygrps in your .mdp so that g_energy can give you some useful output for further testing. Look at your [ pairs ] section in your .itp file. Those are the source of the LJ-14 and Coulomb-14 energies. >and what I understood from articles on OPLS force field that it scale down >the LJ-14 and Coulomb-14 energy my a factor of two? as it is specify in >ffoplsaa.itp file >what about GROMOS96 force field, it is mention in manual (Chapter 4 page >no 75) it also scale down the LJ-14 repulsion term . >what I understood by manual that It uses separate parameter for LJ-14 >interaction Is it is correct? If yes then It uses separate parameters only >for LJ repulsive term or all the non bonded terms i.e. LJ repulsive,LJ >attractive and for coulomb term? The .itp file for your molecules will have the information that you are after. 1. The [ pairs ] section is a list that defines what 1-4 interactions exist. If a 1-4 pair is not in the [ pairs ] section, LJ-14 and Coulomb-14 interactions will not be included in the energies. **That's a good test for you right there. Remove all entries from the [ pairs ] section and your 1-4 energies should drop to zero. 2. The charges for 1-4 interactions are the normal ones, and FudgeQQ will be applied. 3. The LJ sigma / epsilon parameters will be taken from [ pairs ] if they are there, or (second in hiearchy) from [ pairtypes ] if they are there, or (third in hiearchy) generated from the regular non-bonded parameters if gen-pairs=yes. In this third case, FudgeLJ is applied. Each force-field has its own rules (e.g. gen-pairs and FudgeLJ/QQ), but these apply to the information outlined above. For example, gen-pairs does NOT mean "generate a [ pairs ] section for the molecule." Instead, it means "If LJ-14 epsilon and sigma are not present in a [ pairs ] section entry, and that type of interaction is not explicitly formulated in [ pairtypes ], then it is permissible to use the regular non-bonded parameters, and in that case scale them by FudgeLJ." OPLS-AA uses gen-pairs=yes, Force-fields that use gen-pairs=no (GROMOS96 I think) will have a very large [ pairtypes ] section. FudgeLJ is not used when gen-pairs=no, but FudgeQQ is always used. Note that it is perfectly reasonable to scale the 1-4 FudgeQQ/LJ and set gen-pairs=no. If there is still misunderstanding, do a search for {pairs pairtypes}. Also, if your main concern is ensuring that you don't have any 1-4 interactions where you shouldn't then I would recommend drawing out your molecule and making sure that you don't have any RB dihedrals defined with an overlapping entry in the [ pairs ] section. However, this is not absolutely going to work because it gets complicated sometimes. Eg: I have yet to figure out exactly why things are treated as they are in the [ pairs ] section for two non-RB double-bonded carbons in the middle of a long chain of RB carbons :: more specifically I am referring to lipid acyl chains with a double bond (for example pope.itp from Dr. Tieleman). Chris. From kwichapong at gmail.com Tue Sep 12 10:00:33 2006 From: kwichapong at gmail.com (kanin wichapong) Date: Tue, 12 Sep 2006 10:00:33 +0200 Subject: [gmx-users] merge ligand and protein Message-ID: <172bb8a80609120100m5087b764h645ee49d38fc063d@mail.gmail.com> Dear All I tried to merge the ligand togethere with the protein by using pdb2gmx. However, it doesn't work. Is there another way to merge ligand and protein together. Thank you so much for all of the answers Best Regard Kanin -------------- next part -------------- An HTML attachment was scrubbed... URL: From Florian.Haberl at chemie.uni-erlangen.de Tue Sep 12 10:13:44 2006 From: Florian.Haberl at chemie.uni-erlangen.de (Florian Haberl) Date: Tue, 12 Sep 2006 10:13:44 +0200 Subject: [gmx-users] merge ligand and protein In-Reply-To: <172bb8a80609120100m5087b764h645ee49d38fc063d@mail.gmail.com> References: <172bb8a80609120100m5087b764h645ee49d38fc063d@mail.gmail.com> Message-ID: <200609121013.44474.Florian.Haberl@chemie.uni-erlangen.de> On Tuesday 12 September 2006 10:00, kanin wichapong wrote: > Dear All > I tried to merge the ligand togethere with the protein by using > pdb2gmx. However, it doesn't work. Is there another way to merge ligand and > protein together. > Thank you so much for all of the answers take a look at http://www.gromacs.org/gromacs/documentation/tutorial.html John Kerrigans drug/enzyme tutorial and another GROMACS intro > > Best Regard > Kanin -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) ? 9131 ? 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- From tsjerkw at gmail.com Tue Sep 12 12:37:03 2006 From: tsjerkw at gmail.com (Tsjerk Wassenaar) Date: Tue, 12 Sep 2006 12:37:03 +0200 Subject: [gmx-users] Re: genion causing atom to be in multiple T-Coupling groups In-Reply-To: <45056BF4.3030402@xray.bmc.uu.se> References: <20060911131005.D49BE2407C@xray.bmc.uu.se> <45056BA0.3080808@ucd.ie> <45056BF4.3030402@xray.bmc.uu.se> Message-ID: <8ff898150609120337y150ea10fybd44d59e5ff74ea2@mail.gmail.com> Una, In your case you can also try the T-coupling groups Protein and Non-Protein, without providing a .ndx file. However, in general give some thoughts to temperature coupling (groups) when setting up your system and try to grasp how groups are treated in gromacs. Hope it helps, Tsjerk On 9/11/06, David van der Spoel wrote: > Una Bjarnadottir wrote: > > Una Bjarnadottir wrote: > > > >>> Dear Users, > >>> > >>> I'm hoping for an answear on my problem with neutralizing my system > >>> adding 3 Cl ions with genion. When running grompp after genion with > >>> the new generated .gro file I get this error: > >>> > >>> Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1) > >>> > >>> which is the last water atom (total in system 33003) and groups 15 > >>> and 1 are Cl and protein groups if I on the other hand do not > >>> neutralize the system the run goes fine! When looking into the .ndx > >>> file atom 33000 is in 4 groups; 0 (system), 11 (non-protein), 14 > >>> (SOL) and 16 (other). How can I change the group definitions and > >>> make sure the groups do not overlap and to be unique? > >>> It seems to be something wrong with how the genion works for me. I > >>> followed the tutorial and chose the SOL group and water molecules > >>> were replaced by the Cl ions. Than I modifyed the .top file and took > >>> 3 sol molecules and added the 3 ions. > >>> > >>> Please help because have not been able to fix the problem with > >>> related letters on the subject on the list. > >>> > >>> Best regards, Una Bjarnadottir > >>> > >> > >> > >>> What do your tcoupl groups look like? > > > > tc-grps':'Protein OTHER CL- ###where I have to call SOL: OTHER > > otherwise error > > > >>> Could it be System SOL? > > > >>> The number may be confusing, you should subtract one from them when > >>> compared to the output from gmxcheck -n index.ndx > >>> So it seems that atom 33000 (numbering in the coordinate file) is in > >>> groups 14 and 0. Maybe you should make a new index file after genion. > >>> Note that it is good practice to make the ions part of the solvent T > >>> coupling group. > > > > I made the indes file after running genion using the .gro output file > > from genion generating it. Also I thought you would have to subtract > > one and it was groups 14 and 0 instead of 15 and 1. How would I have > > the ions part of the solvent T coupling group? By modifying the .top > > file to [ molecules ] > > ; Compound #mols > > Protein_E 1 > > Protein_I 1 > > Protein_A 1 > > SOL+CL- 9719 > > > > and than the tc-grps in the .mdp file accordingly to that. How will I > > define SOL and CL- together, I tryed SOL+CL- and SOL-CL- but Fatal > > error: No such moleculetype SOL+CL- came for both. > > Best regards David for your reply, Una David. > > in make_ndx you type > 14 | 15 > that will give you the combination of the two groups (if 14 is SOL and > 15 is CL-) > > > > > _______________________________________________ > > gmx-users mailing list gmx-users at gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the www > > interface or send it to gmx-users-request at gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 From kwichapong at gmail.com Tue Sep 12 13:40:59 2006 From: kwichapong at gmail.com (kanin wichapong) Date: Tue, 12 Sep 2006 13:40:59 +0200 Subject: [gmx-users] merger ligand and protein to constriant Message-ID: <172bb8a80609120440y37edcb8ai95e1bfcb0e620944@mail.gmail.com> Hi all I already look in the turorial however that is not the thing that I try to look for. I would like to merge the ligand into the protein and then make the contrain between two atoms, one from the liagand and one from the protein. However, as far as I know, I can do the constraint or restraint just in the one chain. I cant do that with the different chain. So that i try to merge ligand chain and protein chain. I tried to do that with pdb2gmx but it is not work. So that i would like to know is there any way to merge the ligand chain with the protein chain. Thanks for all your suggstions Best Regard Kanin -------------- next part -------------- An HTML attachment was scrubbed... URL: From wangzhun at pumc.edu.cn Tue Sep 12 14:07:37 2006 From: wangzhun at pumc.edu.cn (=?gb2312?B?zfXXvA==?=) Date: Tue, 12 Sep 2006 20:07:37 +0800 Subject: [gmx-users] merger ligand and protein to constriant Message-ID: <358062857.10180@pumc.edu.cn> What about merging the ligand the the protein by DeepView? In your mail: >From: "kanin wichapong" >Reply-To: Discussion list for GROMACS users >To: gmx-users at gromacs.org >Subject: [gmx-users] merger ligand and protein to constriant >Date:Tue, 12 Sep 2006 13:40:59 +0200 > >Hi all > I already look in the turorial however that is not the thing that I try to >look for. I would like to merge the ligand into the protein and then make >the contrain between two atoms, one from the liagand and one from the >protein. However, as far as I know, I can do the constraint or restraint >just in the one chain. I cant do that with the different chain. So that i >try to merge ligand chain and protein chain. I tried to do that with pdb2gmx >but it is not work. So that i would like to know is there any way to merge >the ligand chain with the protein chain. > Thanks for all your suggstions > >Best Regard >Kanin >_______________________________________________ >gmx-users mailing list gmx-users at gromacs.org >http://www.gromacs.org/mailman/listinfo/gmx-users >Please don't post (un)subscribe requests to the list. Use the >www interface or send it to gmx-users-request at gromacs.org. >Can't post? Read http://www.gromacs.org/mailing_lists/users.php From bjorn.windshugel at uku.fi Tue Sep 12 14:35:39 2006 From: bjorn.windshugel at uku.fi (Bjoern Windshuegel) Date: Tue, 12 Sep 2006 15:35:39 +0300 Subject: [gmx-users] merger ligand and protein to constriant In-Reply-To: <172bb8a80609120440y37edcb8ai95e1bfcb0e620944@mail.gmail.com> References: <172bb8a80609120440y37edcb8ai95e1bfcb0e620944@mail.gmail.com> Message-ID: <200609121535.39520.bjorn.windshugel@uku.fi> Hi, you can also have different chains (Protein and Ligand) and constrain them. Using the -merge option you can merge the ligand into the protein but for that you need the topology for the ligand (as rtf, not from prodrg). If you use Prodrg-topology you first set up the protein without ligand. Then you include the topology for the ligand into the protein topology (#include XXX.top) and also the coordinates in the protein-gro-file. Then you can proceed with adding water, ions, etc. Then you can also apply position-restraints. By the way, as far as I know Sonja Schlimme has used a similar kind of setup in her MD simulations. So you could also ask her. Best regards, Bj?rn > Hi all > I already look in the turorial however that is not the thing that I try > to look for. I would like to merge the ligand into the protein and then > make the contrain between two atoms, one from the liagand and one from the > protein. However, as far as I know, I can do the constraint or restraint > just in the one chain. I cant do that with the different chain. So that i > try to merge ligand chain and protein chain. I tried to do that with > pdb2gmx but it is not work. So that i would like to know is there any way > to merge the ligand chain with the protein chain. > Thanks for all your suggstions > > Best Regard > Kanin -- Bj?rn Windsh?gel Department of Pharmaceutical Chemistry University of Kuopio Harjulantie 1 70211 Kuopio, FINLAND Phone: (+358) 17 162463 Fax: (+358) 17 162456 From wurl04 at iccas.ac.cn Tue Sep 12 15:23:16 2006 From: wurl04 at iccas.ac.cn (Rongliang Wu) Date: Tue, 12 Sep 2006 21:23:16 +0800 Subject: [gmx-users] cross terms!! Message-ID: <20060912132314.EA52C687@elvira.its.uu.se> hello,gmx-users yes! thanks david!! where and how the cross terms, like bond-bond and bond-angle cross potential terms, designated in the parameter file. the mannual had these potential functions but i don't know how to switch it off, so as to make the parameter for my system the same with those in literature. regards! thanks! ????????Rongliang Wu ????????wurl04 at iccas.ac.cn ??????????2006-09-12 From spoel at xray.bmc.uu.se Tue Sep 12 15:26:05 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Tue, 12 Sep 2006 06:26:05 -0700 Subject: [gmx-users] cross terms!! In-Reply-To: <20060912132314.EA52C687@elvira.its.uu.se> References: <20060912132314.EA52C687@elvira.its.uu.se> Message-ID: <4506B56D.6010209@xray.bmc.uu.se> Rongliang Wu wrote: > hello,gmx-users > yes! thanks david!! > > where and how the cross terms, like bond-bond and bond-angle cross potential terms, designated in the parameter file. > the mannual had these potential functions but i don't know how to switch it off, so as to make the parameter for my system > the same with those in literature. > not sure I understand what you mean. best thing to try is to write a topology file, run grompp and then with gmxdump -s topol.tpr | less you check whether the parameters are interpreted correctly by grompp. these functions have not been excessively tested, so please compare results carefully! > regards! > > thanks! > > > ????????Rongliang Wu > ????????wurl04 at iccas.ac.cn > ??????????2006-09-12 > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From alokjain at iitk.ac.in Tue Sep 12 16:49:30 2006 From: alokjain at iitk.ac.in (alokjain at iitk.ac.in) Date: Tue, 12 Sep 2006 20:19:30 +0530 (IST) Subject: [gmx-users] RB dihedral potential query in OPLS In-Reply-To: <1158039233.450646c1b2442@webmail.utoronto.ca> References: <1158039233.450646c1b2442@webmail.utoronto.ca> Message-ID: <38186.172.28.124.187.1158072570.squirrel@newwebmail.iitk.ac.in> hello gmx users, First of all thanks to Chris for his response to my previous mail.But I still have a doubt regarding RB potential which I would like to get clarified about. I would be very thankfull if you can go through my post (patiently) and comment on it. ___________________________________________ Gromacs 3.2 manual states " The use of RB potential implies exclusion of LJ interactions between the first and the last atom of the dihedral..." I also searched the mailing list and came accross a response from David to one of the queries which is as follows: "The original Ryckaert Bellemans potential is for carbon tails only (e.g. decane, or lipids). The same potential is used in OPLS but with different parameters in which the(scaled) pair interaction is part of the parameterization" http://www.gromacs.org/pipermail/gmx-users/2004-May/010500.html Gromacs 3.3 manual along with the above mentioned statement in manual 3.2 also states that: "Ryckaert-Bellemans potentials are also used in e.g. the OPLS force field in combination with 1-4 interactions. You should therefore not modify topologies generated by pdb2gmx in this case". ------------------------------------------------------------ I presently ran a MD simulaiton of a protein solvated in water using gromacs 3.2.1 and OPLS-AA force filed.A energy output in the log file looks like: Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 1.15231e+03 2.92374e+03 1.73760e+02 1.32334e+03 1.86599e+03 Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR) 5.03326e+03 1.39004e+05 -1.66722e+03 -9.54632e+05 -5.37046e+04 Potential Kinetic En. Total Energy Temperature Pressure (bar) -8.58528e+05 1.57277e+05 -7.01250e+05 3.04174e+02 -4.80269e+01 So I have a Ryckaert-Bell. energy term for Proper dihedral potential. I also have a 14 terms for LJ and Coulomd energy. My initial impression was that once we use the RB dihedral term,we may actually not get the 14 term in my energy profile (Manual 3.2) But after going through the manual 3.3 and also Divid's post,I suppose that the parameters in OPLS-AA are so defined that RB potential along with the 14 interactions (scaled) are calculated seperately. Is this the case????? PS: Chris suggested me to check the [pairs] and [dihedral] entry in the *.top (*.itp) file which I did and I found identical atoms in both the entries which according to Chris should not be the case...So I am more confused. Regards. Alok Jain. > >>In manual (chapter 4 page no 62) it was written The use of RB potential >>implies exclusion of LJ interaction between first and the last atom of >> the >>dihedral (mean 1-4 interaction).So why I am getting LJ-14 and Coulomb-14 >>energy in my log file (see below) is there is any problem in this >>simulation or it is normal? > > Only the 1-4 interactions spanning RB potentials should be excluded from > LJ-14 > and coulomb-14. For example, lipid headgroups may be treated without RB's > and > the acyl chains treated with RB's. If you want to see where things are > coming > from, make an index file and then use enerygrps in your .mdp so that > g_energy > can give you some useful output for further testing. Look at your [ pairs > ] > section in your .itp file. Those are the source of the LJ-14 and > Coulomb-14 > energies. > >>and what I understood from articles on OPLS force field that it scale >> down >>the LJ-14 and Coulomb-14 energy my a factor of two? as it is specify in >>ffoplsaa.itp file >>what about GROMOS96 force field, it is mention in manual (Chapter 4 page >>no 75) it also scale down the LJ-14 repulsion term . >>what I understood by manual that It uses separate parameter for LJ-14 >>interaction Is it is correct? If yes then It uses separate parameters >> only >>for LJ repulsive term or all the non bonded terms i.e. LJ repulsive,LJ >>attractive and for coulomb term? > > The .itp file for your molecules will have the information that you are > after. > 1. The [ pairs ] section is a list that defines what 1-4 interactions > exist. If > a 1-4 pair is not in the [ pairs ] section, LJ-14 and Coulomb-14 > interactions > will not be included in the energies. > > **That's a good test for you right there. Remove all entries from the [ > pairs ] > section and your 1-4 energies should drop to zero. > > 2. The charges for 1-4 interactions are the normal ones, and FudgeQQ will > be > applied. > 3. The LJ sigma / epsilon parameters will be taken from [ pairs ] if they > are > there, or (second in hiearchy) from [ pairtypes ] if they are there, or > (third > in hiearchy) generated from the regular non-bonded parameters if > gen-pairs=yes. > In this third case, FudgeLJ is applied. > > Each force-field has its own rules (e.g. gen-pairs and FudgeLJ/QQ), but > these > apply to the information outlined above. For example, gen-pairs does NOT > mean > "generate a [ pairs ] section for the molecule." Instead, it means "If > LJ-14 > epsilon and sigma are not present in a [ pairs ] section entry, and that > type of > interaction is not explicitly formulated in [ pairtypes ], then it is > permissible to use the regular non-bonded parameters, and in that case > scale > them by FudgeLJ." > > OPLS-AA uses gen-pairs=yes, Force-fields that use gen-pairs=no (GROMOS96 I > think) will have a very large [ pairtypes ] section. FudgeLJ is not used > when > gen-pairs=no, but FudgeQQ is always used. Note that it is perfectly > reasonable > to scale the 1-4 FudgeQQ/LJ and set gen-pairs=no. > > If there is still misunderstanding, do a search for {pairs pairtypes}. > > Also, if your main concern is ensuring that you don't have any 1-4 > interactions > where you shouldn't then I would recommend drawing out your molecule and > making > sure that you don't have any RB dihedrals defined with an overlapping > entry in > the [ pairs ] section. However, this is not absolutely going to work > because it > gets complicated sometimes. Eg: I have yet to figure out exactly why > things are > treated as they are in the [ pairs ] section for two non-RB double-bonded > carbons in the middle of a long chain of RB carbons :: more specifically I > am > referring to lipid acyl chains with a double bond (for example pope.itp > from Dr. > Tieleman). > > Chris. > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > From chris.neale at utoronto.ca Tue Sep 12 19:44:42 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Tue, 12 Sep 2006 13:44:42 -0400 Subject: [gmx-users] re: RB dihedral potential query in OPLS Message-ID: <1158083082.4506f20ae9fda@webmail.utoronto.ca> Those OPLS-AA "Ryckaert Bellemans" terms are intended to work with [ pairs ]. They are not the same as the real RB terms. Here is a good explaination: http://www.gromacs.org/pipermail/gmx-users/2004-May/010500.html "The original Ryckaert Bellemans potential is for carbon tails only (e.g. decane, or lipids). The same potential is used in OPLS but with different parameters in which the (scaled) pair interaction is part of the parameterization." My appologies for leading you astray earlier, I thought you were refering to RB terms in lipid tails. Chris. From alfem at ula.ve Tue Sep 12 22:39:36 2006 From: alfem at ula.ve (Alvaro Fernandez) Date: Tue, 12 Sep 2006 16:39:36 -0400 (VET) Subject: [gmx-users] CVS password Message-ID: <39173.150.185.128.20.1158093576.squirrel@azmodan.ula.ve> Hi, I executed this command : cvs -z3 -d :ext:@cvs.gromacs.org:/home/gmx/cvs co gmx But I don't have the password. What is the password? Thanks. ALVARO FERNANDEZ ``````````````````````````````````````` GRUPO DE QU?MICA TE?RICA: /\\ PROCESOS DIN?MICOS EN QU?MICA |()|| \// Facultad de Ciencias - ULA La Hechicera, M?rida-5101 - Vlza. From svb1 at msstate.edu Tue Sep 12 21:57:27 2006 From: svb1 at msstate.edu (svb1 at msstate.edu) Date: Tue, 12 Sep 2006 14:57:27 -0500 Subject: [gmx-users] Fatal error: Force field inconsistency Message-ID: <1158091046.45071127025ef@webmail.msstate.edu> Hello, I had this error while trying to run a simulation for a small molecule without water and bilayer, I have included in the topol.top its parameters taken from OPLS and its topology, since I did not created the topology with the pdb2gmx I did not included the ffoplsa.itp in the topol, however after grompp -norenum ?debug, and mdrun I got the following message Fatal error: Force field inconsistency: 1-4 interaction parameters for atoms 9-10 not the same as for other atoms with the same atom type. I already checked the [pairs] and found that for the same type of atoms the parameters are the same . so why is giving me this error?. It doesn't make sense. I read in the GROMACS mailing list that including -norenum with grompp, it make work but it did not, so what I did was to commented out the 9-10 pair interaction from [pairs], but still the same error, then I comented out [pairs] and all the 1-4 interactions defined in [pairs] in my molecule.itp, and after grompp and mdrun the system did not complain. The thing is that now it is calculating the 1-4 interactions from the molecule parameters in molecule.itp [which has the parameters and topology], with :[ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 1 yes 1.0 0.5 because the explicit [pairs ] were comented out due to the Fatal error: Force field inconsistency. Can somebody give an advice, some people had this problem posted on the web, but I couldn't find the solution for my eventhought we all get the same error. Thanks, Sandra From james.zhangj at gmail.com Wed Sep 13 03:10:18 2006 From: james.zhangj at gmail.com (james zhang) Date: Tue, 12 Sep 2006 21:10:18 -0400 Subject: [gmx-users] running CPMD with GROMACS interface in SGI irix 6.5 Message-ID: <93e2edd90609121810x3631409fy8e44a8a78c346997@mail.gmail.com> Hi I got some trouble in running CPMD with GROMACS interface in SGI irix 6.5. Thanks in advance the error is [PEAK NUMBER 116] PEAK MEMORY 14169180 = 113.4 MBytes [ALL. NUMBER 116] TOTAL MEMORY 13983696 = 111.9 MBytes ================================================================== PROGRAM STOPS IN SUBROUTINE MEMORY_CHECK| CORRUPTED MEMORY [PROC= 8] EIGV 390897072 CORRUPTED 390994624 CORRUPTED 12193 SC0 390994640 CORRUPTED 391254032 CORRUPTED 32423 PME 391254048 CORRUPTED 391513440 CORRUPTED 32423 GDE 391513456 CORRUPTED 391772848 CORRUPTED 32423 HGPOT 391860984 CORRUPTED 392180992 CORRUPTED 40000 HIPZ 392181008 CORRUPTED 394741016 CORRUPTED 320000 NZFFP 394741032 CORRUPTED 396297320 CORRUPTED 194535 NZFSP 396297336 CORRUPTED 396987776 CORRUPTED 86304 396987792 CORRUPTED 403238296 CORRUPTED 781312 403238312 CORRUPTED 416826464 CORRUPTED 1698518 ------------------------------------------------------------------ [PEAK NUMBER 116] PEAK MEMORY 14169180 = 113.4 MBytes [ALL. NUMBER 116] TOTAL MEMORY 13983696 = 111.9 MBytes ================================================================== PROGRAM STOPS IN SUBROUTINE MEMORY_CHECK| CORRUPTED MEMORY [PROC= 9] [PEAK NUMBER 116] PEAK MEMORY 14169180 = 113.4 MBytes [ALL. NUMBER 116] TOTAL MEMORY 13983696 = 111.9 MBytes ================================================================== PROGRAM STOPS IN SUBROUTINE MEMORY_CHECK| CORRUPTED MEMORY [PROC= 10] PC: 0xb18ca40 MPI_SGI_stacktraceback in /usr/lib64/libmpi.so PC: 0xb1b5e30 PMPI_Abort in /usr/lib64/libmpi.so PC: 0xb1e84b8 pmpi_abort_ in /usr/lib64/libmpi.so PC: 0x10624edc stopgm in /home/irix/meen/jzhang/qmmm/CPMD-3.11.1 /SOURCE/cpmd.x PC: 0x1049884c memory_check in /home/irix/meen/jzhang/qmmm/CPMD-3.11.1 /SOURCE/cpmd.x PC: 0x1051866c testex in /home/irix/meen/jzhang/qmmm/CPMD-3.11.1 /SOURCE/cpmd.x PC: 0x10447cd4 updwf in /home/irix/meen/jzhang/qmmm/CPMD-3.11.1 /SOURCE/cpmd.x PC: 0x10399770 interface in /home/irix/meen/jzhang/qmmm/CPMD-3.11.1 /SOURCE/cpmd.x PC: 0x10633614 interpt in /home/irix/meen/jzhang/qmmm/CPMD-3.11.1 /SOURCE/cpmd.x PC: 0x10698438 cpmd in /home/irix/meen/jzhang/qmmm/CPMD-3.11.1/SOURCE/cpmd.x PC: 0x10698510 cpmd_stuttgart in /home/irix/meen/jzhang/qmmm/CPMD-3.11.1 /SOURCE/cpmd.x PC: 0x291fc34 main in /usr/lib64/libftn.so -- Sincerely yours, James jianzhang Department of Mechanical and Chemical Engineering North Carolina Agricultural and Technical State University 1601 East Market Street Greensboro, NC 27411 -- Sincerely yours, James jianzhang Department of Mechanical and Chemical Engineering North Carolina Agricultural and Technical State University 1601 East Market Street Greensboro, NC 27411 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nsapay at ucalgary.ca Wed Sep 13 03:09:40 2006 From: nsapay at ucalgary.ca (Nicolas SAPAY) Date: Tue, 12 Sep 2006 19:09:40 -0600 (MDT) Subject: [gmx-users] CHARMM force field implementation in Gromacs : conversion of periodic into Ryckaert-Bellemans parameters. Message-ID: <33710.136.159.234.195.1158109780.squirrel@136.159.234.195> Hello, I have noticed that both in the Yuguang Mu's and the Mark Abraham's work, the periodic parameters of dihedral angles have been converted into Ryckaert-Bellemans ones. I have tried to find more info about this in the CHARMM and Gromacs documentations but I have not found much. Why exactly this conversion should be done since the periodic potential is implemented in both force fields? My problem is that several dihedral angles cannot be easily converted in RB parameters since their multiplicities is equal to 6 and the RB potential implemetation is limited to 5 constants. Thanks Nicolas -- [ Nicolas Sapay Ph.D. ] University of Calgary, Dept. of Biological Sciences 2500 University Dr. NW, Calgary AB, T2N 1N4, Canada Tel: (403) 220-6869 Fax: (403) 289-9311 From nsapay at ucalgary.ca Wed Sep 13 03:10:27 2006 From: nsapay at ucalgary.ca (Nicolas SAPAY) Date: Tue, 12 Sep 2006 19:10:27 -0600 (MDT) Subject: [gmx-users] CHARMM force field implementation in Gromacs : retrieval of bonded/non-bonded parameters Message-ID: <33712.136.159.234.195.1158109827.squirrel@136.159.234.195> Hello, I'm trying to use an implementation of the CHARMM force fields in Gromacs and I'm still a little bit confused about how Gromacs retrieves the bonded/non-bonded parameters when the .top file is created. Concretely, I have : 1. a ffcharmmnb.itp where I have defined specific 1-4 LJ parameters in the [pairtypes] section 2. a ffcharmmbon.itp where I have defined bonded parameters 3. a ffcharmm.rtp where I have defined the topology of amimo acids, etc. Since the [bonds], [angles], [dihedral] sections are optional in the .rtp file, I haven't defined them. How all these parameters are taken into account when I generate the .top file with pdb2gmx? When I look in the .top file, I see an [atoms] section but no [bonds] or [pairs] etc. and the charmm ff doesn't seem to be included with an #include command. So, are all my specific 1-4 parameters really taken into account in this case? In fact, I have tried to add somd bonds and improper but that generates a chunk of warnings when I use grompp. Sorry for this basic question but I'm still new in Gromacs... Thanks Nicolas -- [ Nicolas Sapay Ph.D. ] University of Calgary, Dept. of Biological Sciences 2500 University Dr. NW, Calgary AB, T2N 1N4, Canada Tel: (403) 220-6869 Fax: (403) 289-9311 From mark.abraham at anu.edu.au Wed Sep 13 03:52:20 2006 From: mark.abraham at anu.edu.au (Mark Abraham) Date: Wed, 13 Sep 2006 11:52:20 +1000 (EST) Subject: [gmx-users] CHARMM force field implementation in Gromacs : conversion of periodic into Ryckaert-Bellemans parameters. In-Reply-To: <33710.136.159.234.195.1158109780.squirrel@136.159.234.195> References: <33710.136.159.234.195.1158109780.squirrel@136.159.234.195> Message-ID: <36227.150.203.145.27.1158112340.squirrel@sqmail.anu.edu.au> > Hello, > > I have noticed that both in the Yuguang Mu's and the Mark Abraham's work, > the periodic parameters of dihedral angles have been converted into > Ryckaert-Bellemans ones. I have tried to find more info about this in the > CHARMM and Gromacs documentations but I have not found much. Why exactly > this conversion should be done since the periodic potential is implemented > in both force fields? My problem is that several dihedral angles cannot be > easily converted in RB parameters since their multiplicities is equal to 6 > and the RB potential implemetation is limited to 5 constants. To quote my own code comment, "# We need some elaborate functionality to convert the CHARMM dihedral type # of k * (1 + cos(n * xi - delta ) ) functions summed over n into something # GROMACS can implement. While the above functional form exists in # GROMACS, you can't have more than one function of this type, and # CHARMM has a number of dihedral interactions that require more than # one such function. However for delta = 0 or pi and n <= 5, then the above # cosine function can be expanded in powers of cos xi, and the coefficients # of the expansion can be summed in this conversion and presented to # GROMACS as a ready-made Ryckaert-Bellemans dihedral. In practice, this # works because CHARMM only uses such delta and n values for atom type # combinations that need multiple functions of the above form. Warnings # are issued when delta is some other value, and the algorithm dies if # n is > 6. In order to simplify GROMACS logfile output so that it only # has to report one sort of dihedral term for most simulations, all # dihedral terms with n <= 5 are expressed as R-B, even when not necessary. # Dihedrals with n=6 are left in periodic form, since it is not possible # to convert these to R-B form when the summation is limited to the # fifth power of cos xi." So if you have a single dihedral over a set of atoms that has n>=6 then you can leave it in periodic form and the only cost is that you have to remember that the output will likely have both periodic and R-B dihedrals. If you have one such a dihedral in combination with others n<6 then you can use a combination of periodic and R-B. If you have multiple dihedrals with n>=6 you will need to hack the source code, except in some trivial cases, perhaps. Mark From mark.abraham at anu.edu.au Wed Sep 13 04:03:29 2006 From: mark.abraham at anu.edu.au (Mark Abraham) Date: Wed, 13 Sep 2006 12:03:29 +1000 (EST) Subject: [gmx-users] CHARMM force field implementation in Gromacs : retrieval of bonded/non-bonded parameters In-Reply-To: <33712.136.159.234.195.1158109827.squirrel@136.159.234.195> References: <33712.136.159.234.195.1158109827.squirrel@136.159.234.195> Message-ID: <40281.150.203.145.27.1158113009.squirrel@sqmail.anu.edu.au> > Hello, > > I'm trying to use an implementation of the CHARMM force fields in Gromacs > and I'm still a little bit confused about how Gromacs retrieves the > bonded/non-bonded parameters when the .top file is created. Concretely, > I have : > 1. a ffcharmmnb.itp where I have defined specific 1-4 LJ parameters in the > [pairtypes] section > > 2. a ffcharmmbon.itp where I have defined bonded parameters > > 3. a ffcharmm.rtp where I have defined the topology of amimo acids, etc. > Since the [bonds], [angles], [dihedral] sections are optional in the .rtp > file, I haven't defined them. > > How all these parameters are taken into account when I generate the .top > file with pdb2gmx? Section 5.5.1 of the manual describes the behaviour of pdb2gmx in interpreting the contentes of the .rtp file in conjunction with the .itp files. > When I look in the .top file, I see an [atoms] section > but no [bonds] or [pairs] etc. In particular, you will read there that angles are automatically generated. Perhaps that should be amened to include the proviso that they are automatically generated only between pairs of bonds. Since you have defined no bonds, you will get nothing else. > and the charmm ff doesn't seem to be > included with an #include command. So, are all my specific 1-4 parameters > really taken into account in this case? In fact, I have tried to add somd > bonds and improper but that generates a chunk of warnings when I use > grompp. Go back and try adding bonds to your .rtp and see how you go. Cheers, Mark From chris.neale at utoronto.ca Wed Sep 13 05:08:45 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Tue, 12 Sep 2006 23:08:45 -0400 Subject: [gmx-users] A method to scale Coulombic 1-4 interactions seperately Message-ID: <1158116925.4507763d418e9@webmail.utoronto.ca> There is a recent publication about combining the Berger lipids with OPLS-AA and getting the correct 1-4 scaling factor. New dihedrals were developed because it is possible to set special 1-4 parameters for LJ, but not coulomb. However, there is another workaround to this that should be generally applicable to 1-4 coulombic scaling. The lipids.itp file has already defined [ pairtypes ] so the LJ 1-4 is scaled correctly (FudgeLJ will not be applied to the values in [ pairtypes ]). The problem now is that OPLS-AA requires a FudgeQQ of 0.5 and the Berger lipids desire a FudgeQQ of one. The solution comes in two parts: 1. Divide the epsilon entries in the [ pairtypes ] of lipid.itp by 2.0. Now the LJ and coulombic 1-4 interactions are both exactly half of what they should be. 2. Every entry in the [ pairs ] section of pope.itp should appear twice. Now the LJ and coulombic 1-4 interactions are both exactly what they should be. This solution should work for an arbitrary 1-4 scaling problem, just make sure that you get the ratios correct. A detailed method is outlined below and that is followed by the method that I used to test this procedure. I have also run a 0.5ns simulation and the system "looks" fine (when I say looks fine I mean by visual inspection or by g_density). 0.5ns is not nearly long enough to properly evaluate area per lipid, but for what it's worth I get 0.53nm^2 per lipid with regular combination rules and 0.52nm^2 per lipid with the half-epsilon-double-pair method outlined here. Perhaps the Gromacs crew could tell us whether a double [ pairs ] entry might run into problems in any special situations? ##################################################### Method to change your files: 1. I assume that OPLS-AA + Berger lipid users have done something similar to this: http://www.gromacs.org/pipermail/gmx-users/2006-May/021416.html 2. copy ffoplsaa.itp to ffoplsaa_mod.itp and edit the new file to contain entries like this: [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 3 yes 0.5 0.5 #include "/dir/ffoplsaanb_mod.itp" #include "/dir/ffoplsaabon.itp" 3. copy ffoplsaanb.itp to ffoplsaanb_mod.itp and edit the new file to contain entries like this: ;Here are the unmodified atomtypes from lipid.itp LO LO 1 15.9994 0.000 A 2.96000e-01 8.87864e-01 ;carbonyl O, OPLS LOM LOM 1 15.9994 0.000 A 2.96000e-01 8.87864e-01 ;carbonyl O, OPLS ;... ;Here are the original parameters from lipid.itp that have been moved directly to this file. Note that these parameters are commented out and could be removed. ;[ pairtypes ] ; i j funct sigma epsilon ; LO LO 1 2.96E-01 1.10E-01 ; LO LOM 1 2.96E-01 1.10E-01 ;.... ;Here are the parameters from above where epsilon has been divided by 2.0 [ pairtypes ] ; i j funct sigma epsilon LO LO 1 2.96E-01 5.50E-02 LO LOM 1 2.96E-01 5.50E-02 ;.... 4. Copy your lipid topology file (e.g. pope.itp) and, in the new version, copy the [ pairs ] section to right underneath itself (without the [ pairs ] header) If it looked like this first (pope.itp): [ pairs ] 4 7 1 5 8 1 6 9 1 It should look like this after (pope_mod.itp): [ pairs ] ;Here is the first copy 4 7 1 5 8 1 6 9 1 ; Here is the second copy. Only use this with the modified LJ-14 epsilon values 4 7 1 5 8 1 6 9 1 5. Your run .top file should look like this: ; Include forcefield parameters #include "/dir/ffoplsaa_mod.itp" ; Include topologies #include "/dir/pope_mod.itp" [ system ] ... ##################################################### TESTING: Use a system with a protein inserted into a membrane and solvated. OPLS-AA rules. 1. Do a run with nsteps=0 for the original setup and for the new setup 2. gmxdump the .trr file 3. diff the two gmxdumps The only differences are in the forces section and they only apply to atoms in the [ pairs ] section that have been intentionally modified. For example, in pope.itp I get different forces for all atoms except: H1,H2,H3, C17, C20-C31, C36, C39-CA2 There is no difference for some of these because they are not in the [ pairs ] list at all: H1,H2,H3,C20-C23,C25-C31,C39-CA2 There is no difference for some others because one of the parteners in the pair has a charge of zero: C17 in [ pair ] 13 17 (LH1 LP2; LP2 has zero charge) C36 in [ pair ] 32 36 (LC2 LP2; LP2 has zero charge) C24 in [ pair ] 24 27 (LP2 LH1; LP2 has zero charge) C25 in [ pair ] 22 25 (LH1 LP2; LP2 has zero charge) Remember that the LJepsilon was divided by 2 so with double inclusion the Lj portion is not changed at all. This is a decent internal test also because if we had accidentally modified the effective LJ1-4 parameters [(regular/2.0 and include twice) vs. (regular)] then we should have seen force differences for these last four atoms (C17,C36,C24,C25). ##################################################### Here is the .mdp from the test outlined above: title = seriousMD cpp = /home/cneale/exe/cpp integrator = md nsteps = 0 tinit = 0 dt = 0.002 comm_mode = linear nstcomm = 1 comm_grps = System nstxout = 1 nstvout = 1 nstfout = 1 nstlog = 1 nstlist = 10 nstenergy = 1 nstxtcout = 1 ns_type = grid pbc = xyz coulombtype = PME rcoulomb = 0.9 fourierspacing = 0.12 pme_order = 4 vdwtype = cut-off rvdw_switch = 0 rvdw = 1.4 rlist = 0.9 DispCorr = no Pcoupl = Berensden pcoupltype = semiisotropic compressibility = 4.5e-5 4.5e-5 ref_p = 1. 1. tau_p = 4.0 4.0 tcoupl = Berendsen tc_grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300. 300. annealing = no gen_vel = yes gen_temp = 300. gen_seed = 9896 constraints = all-bonds constraint_algorithm= lincs lincs-iter = 1 lincs-order = 4 From sir_donald_bradman at yahoo.com Wed Sep 13 05:31:49 2006 From: sir_donald_bradman at yahoo.com (Manohar Murthi) Date: Tue, 12 Sep 2006 20:31:49 -0700 (PDT) Subject: [gmx-users] wham question In-Reply-To: <20060913015304.023EC2407E@xray.bmc.uu.se> Message-ID: <20060913033149.78506.qmail@web51002.mail.yahoo.com> hi all does anyone have an example/tutorial of how to do umbrella sampling using gromacs & wham? i'm about to try to calculate free energies of binding using this method. i can find no information whatsoever about 'wham.gct', which is an optional input mentioned in the mdrun online reference page. what is this file supposed to contain? i've yet to actually try it, but setting up the other input files seems relatively straightforward. i'm hoping to benefit from others' experience to figure out how to choose and vary the harmonic force constants for the different umbrella runs. any advice would be greatly appreciated. cheers mo __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From zgxjlx at gmail.com Wed Sep 13 05:39:45 2006 From: zgxjlx at gmail.com (liu xin) Date: Wed, 13 Sep 2006 11:39:45 +0800 Subject: [gmx-users] Re: Simulation problem with extended membrane system! In-Reply-To: <1157733305.45019bb953127@webmail.utoronto.ca> References: <1157733305.45019bb953127@webmail.utoronto.ca> Message-ID: If I solvate my GPCR into the DPPC128 system using genbox, there are only about 50 lipids left, which I think are too few, so I want a larger starting structure. According to your note, when I did step 3, loaded my DPPC183 system to VMD, I found the edges lined up poorly, there is are gaps between two periodic cells. I also try other system like DPPC200, DPPC150, but only the original dppc128 system, I've equilibrated it for 2ns, have no gap between two periodic cells. So, I will try another starting structure, like POPC, DMPC or your POPE. But I still can't figure out why there are gaps when using genbox to extend the DPPC system. On 9/9/06, chris.neale at utoronto.ca wrote: > > >According to your suggestion, I did a energy minimization and then a MDS > >with "freezegrps=SOL, freezedim=N, N, Y", the rest of the system were > >simulated with no constraint. This time I use semiisotropic pressure > >coupling with tau_p=5. The system will be equilibrated with water > >constrained for 1ns, do you think it's enough? > > It will be more than enough. Use vmd to watch the trajectory. It's > important > actually look at the structures. > > >The reason why I want to extend the system is because that I've got a > GPCR, > >and I want to simulate it in a DPPC membrane environment, but the z > >dimension of the membrane, downloaded from Dr. Tielman's websit, was not > > >large enough, when I align the protein to the z axis of the membrane I > find > >the two ends of the protein are poking out of both water layers. > > In this case you may not need to extend the lipid. Why not just use > editconf to > increase the z dimension while keeping the x and y constant. Then insert > your > protein, re-solvate, re-equilibrate, and your into production. If your > lipid > takes up a maximum amout of space D in the xy-plane, then x and y need > only be > equal to [D + 2*max(LJ cutoff, Coulombic real-space cutoff) + some extra > amount > in case the protein fluctuations make it larger during the simulation]. > > >Back to the previous question, after solvate the lipids in water, can I > >remove the water placed in the membrane with excel instead of script? > Cause > >with editconf we can know the z dimension of the lipids_only system, > let's > >say 6, so if I center the whole system with 0 0 0, the water molecules > with > >z coordinates below 3 and above -3 will be excluded. If I'm right, I > think > >excel can do it too, or the scripts have some advantages? > > Sure you can use excel, but I am not sure how that is going to affect your > > formatting or how gromacs responds to formatting (i.e. spaces / tabs / the > number of each) So scrips have 2 advantages: 1)formatting is easily > maintained, > 2)if you need to do it a second time you just type one command. After > using > excel (or a script) make sure to update you topology file to indicate the > number > of waters. > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -------------- next part -------------- An HTML attachment was scrubbed... URL: From chris.neale at utoronto.ca Wed Sep 13 06:03:28 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Wed, 13 Sep 2006 00:03:28 -0400 Subject: [gmx-users] Re: Simulation problem with extended membrane system! Message-ID: <1158120208.4507831024ac2@webmail.utoronto.ca> >If I solvate my GPCR into the DPPC128 system using genbox, there are only >about 50 lipids left, which I think are too few, so I want a larger starting >structure. >According to your note, when I did step 3, loaded my DPPC183 system to VMD, >I found the edges lined up poorly, there is are gaps between two periodic >cells. I also try other system like DPPC200, DPPC150, but only the original >dppc128 system, I've equilibrated it for 2ns, have no gap between two >periodic cells. >So, I will try another starting structure, like POPC, DMPC or your POPE. But >I still can't figure out why there are gaps when using genbox to extend the >DPPC system. It's because any overlap causes an entire lipid to be removed. If you don't want to equilibrate, try exactly doubling your system size in x and y. That should work perfectly. From zzhwise1 at 163.com Wed Sep 13 07:24:15 2006 From: zzhwise1 at 163.com (zzhwise1) Date: Wed, 13 Sep 2006 13:24:15 +0800 (CST) Subject: [gmx-users] how to write a annealing .mdp Message-ID: <450795FF.000026.28970@bj163app52.163.com> hello everyone i want to anneal my system,but i don't konw how to wrote a right annealing-mdp! could anyone give me a moldel? tanks in advaced! -------------- next part -------------- An HTML attachment was scrubbed... URL: From zzhwise1 at 163.com Wed Sep 13 08:38:10 2006 From: zzhwise1 at 163.com (zzhwise1) Date: Wed, 13 Sep 2006 14:38:10 +0800 (CST) Subject: [gmx-users] does the conformation cause this error? Message-ID: <4507A752.00000B.01047@bj163app52.163.com> hi all i have a problem:when i did the mdrun ,it stopped early for error:Maximum force = 9.0996275e+09 on atom 606 Norm of force = 2.8519283e+08 does this cause by the conformation?and how to resolve it? -------------- next part -------------- An HTML attachment was scrubbed... URL: From Mark.Abraham at anu.edu.au Wed Sep 13 08:47:13 2006 From: Mark.Abraham at anu.edu.au (Mark Abraham) Date: Wed, 13 Sep 2006 16:47:13 +1000 Subject: [gmx-users] does the conformation cause this error? In-Reply-To: <4507A752.00000B.01047@bj163app52.163.com> References: <4507A752.00000B.01047@bj163app52.163.com> Message-ID: <4507A971.6020706@anu.edu.au> zzhwise1 wrote: > hi all > i have a problem:when i did the mdrun ,it stopped early for > error:Maximum force = 9.0996275e+09 on atom 606 > Norm of force = 2.8519283e+08 > > does this cause by the conformation?and how to resolve it? Yes. You are probably simulating with a structure that is either non-physical, or not energy-minimized before equilibration. If you haven't tried working through some tutorial material, now might be a good time to consider doing that. Mark From bjorn.windshugel at uku.fi Wed Sep 13 09:40:48 2006 From: bjorn.windshugel at uku.fi (Bjoern Windshuegel) Date: Wed, 13 Sep 2006 10:40:48 +0300 Subject: [gmx-users] "deprecated" In-Reply-To: References: Message-ID: <200609131040.48263.bjorn.windshugel@uku.fi> Hi all, usually I'm using the GROMOS96 force field but for some reason I have to change to the GROMACS force field. Maybe its a stupid question but I'd like to know for what the term "deprecated" stands for when the list ofavailable force fields is presented when using pdb2gmx. According to the dictionary it doesn't sound very promising...;) Best regards, Bj?rn -- Bj?rn Windsh?gel Department of Pharmaceutical Chemistry University of Kuopio Harjulantie 1 70211 Kuopio, FINLAND Phone: (+358) 17 162463 Fax: (+358) 17 162456 From Florian.Haberl at chemie.uni-erlangen.de Wed Sep 13 09:45:04 2006 From: Florian.Haberl at chemie.uni-erlangen.de (Florian Haberl) Date: Wed, 13 Sep 2006 09:45:04 +0200 Subject: [gmx-users] CVS password In-Reply-To: <39173.150.185.128.20.1158093576.squirrel@azmodan.ula.ve> References: <39173.150.185.128.20.1158093576.squirrel@azmodan.ula.ve> Message-ID: <200609130945.06461.Florian.Haberl@chemie.uni-erlangen.de> On Tuesday 12 September 2006 22:39, Alvaro Fernandez wrote: > Hi, > I executed this command : > cvs -z3 -d :ext:@cvs.gromacs.org:/home/gmx/cvs co gmx > But I don't have the password. What is the password? > Thanks. leave it empty it works than. > > > ALVARO FERNANDEZ > ``````````````````````````````````````` > GRUPO DE QU?MICA TE?RICA: > /\\ PROCESOS DIN?MICOS EN QU?MICA > > |()|| > > \// Facultad de Ciencias - ULA > La Hechicera, M?rida-5101 - Vlza. > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Greetings, Florian -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) ? 9131 ? 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- From lindahl at cbr.su.se Wed Sep 13 10:22:17 2006 From: lindahl at cbr.su.se (Erik Lindahl) Date: Wed, 13 Sep 2006 10:22:17 +0200 Subject: [gmx-users] "deprecated" In-Reply-To: <200609131040.48263.bjorn.windshugel@uku.fi> References: <200609131040.48263.bjorn.windshugel@uku.fi> Message-ID: Hi, On Sep 13, 2006, at 9:40 AM, Bjoern Windshuegel wrote: > Hi all, > > usually I'm using the GROMOS96 force field but for some reason I > have to > change to the GROMACS force field. > Maybe its a stupid question but I'd like to know for what the term > "deprecated" stands for when the list ofavailable force fields is > presented > when using pdb2gmx. According to the dictionary it doesn't sound very > promising...;) The "GROMACS" force field was mostly GROMOS87, but with some water- carbon and other nonbonded parameters fixed. There's nothing particularly wrong with it, but there are newer force fields with better performance. However, we've noticed that novice users still picked it because of the "default"-sounding name. In general I recommend people to use GROMOS96, OPLS-AA/L, or Amber (search the mailing list). There are subtle differences among the three, but to some extent that's a matter of taste. Cheers, Erik From navratna.vajpai at unibas.ch Wed Sep 13 10:32:21 2006 From: navratna.vajpai at unibas.ch (Navratna Vajpai) Date: Wed, 13 Sep 2006 10:32:21 +0200 Subject: [gmx-users] Hi... Message-ID: <202973AA-D3F2-40A0-A83A-53DA379505D2@unibas.ch> Dear Eric.. Hi.. This is in regard to your previously replied mail regarding the use of GROMOS96 or OPLS-AA or AMBER force field. As you said it depends upon the users taste which one to use. This means that the three on a broad manner should give convergence of the analyzed data set. Infact from my simulation runs using oplss-aa and gromos96, I didn't found that. I tried using the GROMOS96 and opls-aa force field on my small peptides for a period of 20ns and found that with opls-aa even the phi-psi combination of the individual amino acids were incorrect. Actually this always puzzled me to make a choice for the Force field. The rest of the script was unchanged for the two runs. Could you please comment on the above results? Is there any way really to judge which force field is to be chosen for particular type of analysis? Best regards Nav ******************************************* Navratna Vajpai Ph. D student in Prof. Grzesiek's laboratory Department of Structural Biology Biozentrum, University of Basel Klingelbergstrasse 70, CH-4056 Basel, Switzerland. Phone- +41 61 267 2080(O) +41 78 744 0810(M) navratna.vajpai at unibas.ch -------------- next part -------------- An HTML attachment was scrubbed... URL: From wurl04 at iccas.ac.cn Wed Sep 13 10:48:57 2006 From: wurl04 at iccas.ac.cn (Rongliang Wu) Date: Wed, 13 Sep 2006 16:48:57 +0800 Subject: [gmx-users] the gmxdump reveals less parameters than i expect Message-ID: <20060913084857.212B86C6@elvira.its.uu.se> hello,gmx-users i used grompp to get an tpr and used the gmxdump command to see if the parameters are right, but i found there are less parameters than i expect: functype[12]=ANGLES, thA= 1.09270e+02, ctA= 3.22384e+02, thB= 1.0927 0e+02, ctB= 3.22384e+02 functype[13]=ANGLES, thA= 1.08450e+02, ctA= 3.59227e+02, thB= 1.0845 0e+02, ctB= 3.59227e+02 functype[14]=ANGLES, thA= 1.07740e+02, ctA= 7.53624e+02, thB= 1.0774 0e+02, ctB= 7.53624e+02 functype[15]=ANGLES, thA= 1.18240e+02, ctA= 6.72400e+02, thB= 1.1824 0e+02, ctB= 6.72400e+02 functype[16]=ANGLES, thA= 1.05270e+02, ctA= 1.00483e+03, thB= 1.0527 0e+02, ctB= 1.00483e+03 here, i have 6 types of angles while it told me there are only 5 angle typeps in, and the parameters in the ff*bon.itp are right, the [ angles ] part in the top are also right? why? and i added the parameters in ff*bon.itp to topol.top file and grompp again, the same results are shown. what does this part mean, which is from the gmxdump commmand? regards! thanks! ????????Rongliang Wu ????????wurl04 at iccas.ac.cn ??????????2006-09-13 From YGMu at ntu.edu.sg Wed Sep 13 10:52:46 2006 From: YGMu at ntu.edu.sg (Mu Yuguang (Dr)) Date: Wed, 13 Sep 2006 16:52:46 +0800 Subject: [gmx-users] the gmxdump reveals less parameters than i expect Message-ID: <48BABA4E8A54DF4AAF9CCF36D614027302E1B074@EXCHANGE23.staff.main.ntu.edu.sg> Is it because there are two identical parameters? Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php -----Original Message----- From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Rongliang Wu Sent: Wednesday, September 13, 2006 4:49 PM To: gmx-users Subject: [gmx-users] the gmxdump reveals less parameters than i expect hello,gmx-users i used grompp to get an tpr and used the gmxdump command to see if the parameters are right, but i found there are less parameters than i expect: functype[12]=ANGLES, thA= 1.09270e+02, ctA= 3.22384e+02, thB= 1.0927 0e+02, ctB= 3.22384e+02 functype[13]=ANGLES, thA= 1.08450e+02, ctA= 3.59227e+02, thB= 1.0845 0e+02, ctB= 3.59227e+02 functype[14]=ANGLES, thA= 1.07740e+02, ctA= 7.53624e+02, thB= 1.0774 0e+02, ctB= 7.53624e+02 functype[15]=ANGLES, thA= 1.18240e+02, ctA= 6.72400e+02, thB= 1.1824 0e+02, ctB= 6.72400e+02 functype[16]=ANGLES, thA= 1.05270e+02, ctA= 1.00483e+03, thB= 1.0527 0e+02, ctB= 1.00483e+03 here, i have 6 types of angles while it told me there are only 5 angle typeps in, and the parameters in the ff*bon.itp are right, the [ angles ] part in the top are also right? why? and i added the parameters in ff*bon.itp to topol.top file and grompp again, the same results are shown. what does this part mean, which is from the gmxdump commmand? regards! thanks! ????????Rongliang Wu ????????wurl04 at iccas.ac.cn ??????????2006-09-13 From YGMu at ntu.edu.sg Wed Sep 13 11:04:08 2006 From: YGMu at ntu.edu.sg (Mu Yuguang (Dr)) Date: Wed, 13 Sep 2006 17:04:08 +0800 Subject: [gmx-users] CHARMM force field implementation in Gromacs : conversion of periodic into Ryckaert-Bellemans parameters. Message-ID: <48BABA4E8A54DF4AAF9CCF36D614027302E1B08D@EXCHANGE23.staff.main.ntu.edu.sg> That's why I use a second step to modify the created top file to add such specific dihedral angle explicitly in the top file. >I have noticed that both in the Yuguang Mu's and the Mark Abraham's work, >the periodic parameters of dihedral angles have been converted into >Ryckaert-Bellemans ones. I have tried to find more info about this in the >CHARMM and Gromacs documentations but I have not found much. Why exactly >this conversion should be done since the periodic potential is implemented >in both force fields? My problem is that several dihedral angles cannot be >easily converted in RB parameters since their multiplicities is equal to 6 >and the RB potential implemetation is limited to 5 constants. Thanks Nicolas -- [ Nicolas Sapay Ph.D. ] University of Calgary, Dept. of Biological Sciences 2500 University Dr. NW, Calgary AB, T2N 1N4, Canada Tel: (403) 220-6869 Fax: (403) 289-9311 _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php From qiaobf at gmail.com Wed Sep 13 12:42:37 2006 From: qiaobf at gmail.com (Qiao Baofu) Date: Wed, 13 Sep 2006 12:42:37 +0200 Subject: [gmx-users] Question about parallazing Gromacs Message-ID: <6a91f07b0609130342j5f2f5f8di482c48c9a0e9fb2d@mail.gmail.com> Hi all, I have a question about parallazing gromacs: I run the same system on a cluster of my institute and my local computer, Cluster:* *dual processor boards AMD Opteron 270 (Dual-Core), 2.0 GHz Local computer: AMD X86-64 Cpu, double precision 1. The cluster (nodes=3:ppn=4) runs 87950 MD steps for one hour 2. The cluster (nodes=5:ppn=4) runs 42749 MD steps for one hour 3. The cluster (nodes=11:ppn=4) runs 5962 MD steps for one hour 3. My local computer runs 179090 MD steps For 1hour 51 mintues. It is verry strange that the more cpus I use, the slowest the gromacs runs.!! Who knows what's wrong with my job? And for paralleled gromacs, how many cpus is prefered? The grompp command is: grompp -np 12 -o md3.mdp -c md3in.gro -p MCl.top -o md3.tpr The following is one of the the job scripts on the cluster: # # MD NTP(Berendsen&Berendsen, T=425&P=1bar),200ps tau_p=4 # # #!/bin/bash #PBS -N "md3" # #PBS -l walltime=01:00:00,nodes=3:ppn=4 # #PBS -m abe # #PBS -o md3.out # #PBS -e md3.err # # cd /work/fias/qiao/time_checking/nodes3/ /usr/local/Cluster-Apps/lam/gcc/64/7.1.1/bin/lamboot $PBS_NODEFILE /usr/local/Cluster-Apps/lam/gcc/64/7.1.1/bin/mpirun -np 12 mdrun -v -s md3.tpr -x md3 -e md3 -c md3 -g md3 exit 0 -- Sincerely yours, ********************************************** Baofu Qiao, PhD Frankfurt Institute for Advanced Studies ********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From bjornss at ift.uib.no Wed Sep 13 12:59:50 2006 From: bjornss at ift.uib.no (=?ISO-8859-1?Q?Bj=F8rn?= Steen =?ISO-8859-1?Q?S=E6thre?=) Date: Wed, 13 Sep 2006 12:59:50 +0200 Subject: [gmx-users] Determining onset of melting Message-ID: <1158145190.27910.86.camel@hyperion.ift.uib.no> Hi people, I an relatively new to MD-simulations, having acquainted myself with the GROMACS system for almost a year now. I am using Gromacs 3.3.1(i.e the last stable distribution) I am studying a solid-liquid interface at the moment, in conjunction with some melting simulations, and have some questions I am using the Nose-Hoover thermostat, with coupling time tau_t=0.1ps, and the Parrinello-Rahman barostat with coupling time tau_p=0.5ps, simulating 600000steps at dt=2fs, close to the experimentally measured melting point of the solid(which of course may not correspond well to the melting point in the model system.) My pressure statistics is not very precise, with a typical average of -200+-600Bar(The aimed for pressure being 1Bar, Concerning this I have one questions: 1. How do I make the statistics better without increasing the number of simulation steps? I have already tried several different coupling strengths(times) with no significant improvement in the statistics. I have also tried berendsen pressure coupling, to try avoiding oscillations, with limited success. Any ideas? (Are large pressure fluctuations necessarily unavoidable close to phase-transitions?) I further have some questions regarding analysis of my output 2. What is the best quantitative criteria, easily obtainable in GROMACS for ascertaining onset of melting in a solid crystal where hydrogen bonding is important? I come to think of the following 3 criteria myself: -The rms fluctuations of the atoms from their lattice positions exceeding a certain fraction of the lattice spacing. (Lindemann's criterion)[Phys Rev A 184(1), p. 233-] 3. How can I use the analysis tools(e.g g_rmsf) to get a quick readout of Lindemann's criterion with minimal further processing -The "smearing-out" of peaks in a suitably normalized rdf. 4. Does there exist an objective measure of this valid for solid-liquid transitions in general(something like a width-of-peak measure) , or do I have to construct one for each particular solid-liquid system. -The ratio of hydrogen bonds in the crystal to hydrogen bonds in the liquid, not involved in the crystal bonding configuration. 5. Have I forgotten another relevant measure easily accessible in the Gromacs tools? (Can I use the extent of the qasi-liquid-layer via g_density perhaps?) Any relevant suggestions received with thanks -- --------------------- Bj?rn Steen Saethre PhD-student Theoretical and Energy Physics Unit Institute of Physics and Technology Allegt, 41 N-5020 Bergen Norway Tel(office) +47 55582869 From jaepark at uiuc.edu Wed Sep 13 12:56:06 2006 From: jaepark at uiuc.edu (Jae Hyun Park) Date: Wed, 13 Sep 2006 05:56:06 -0500 (CDT) Subject: [gmx-users] Question about frozen group: Message-ID: <20060913055606.ABT20392@expms1.cites.uiuc.edu> Hi, all GROMACS users: I have a simple question about frozen groups. My simulation system contains a frozen group and several non-frozen groups. Now, I'm testing the effects of mass of frozen atom on non-frozen group dynamics. I compared two simulations - In one case, the frozen atom has finite-mass while in the other, the frozen atom has zero-mass. In both cases, the averaged velocities of non-frozen groups are different. Could anybody explain this happening? I would deeply appreciate any comment. Jae H. Park ======================================= Jae Hyun Park, Ph.D. Postdoctoral Associate 3221 Beckamn Institute University of Illinois at Urbana-Champaign 405 North Mathews Avenue Urbana, IL 61801 (Tel) 217-244-4353, (FAX) 217-244-4333 (E-mail) jaepark at uiuc.edu From jaepark at uiuc.edu Wed Sep 13 12:48:21 2006 From: jaepark at uiuc.edu (Jae Hyun Park) Date: Wed, 13 Sep 2006 05:48:21 -0500 (CDT) Subject: [gmx-users] Question about frozen group: Message-ID: <20060913054821.ABT19035@expms1.cites.uiuc.edu> Hi, all GROMACS users: I have a simple question about frozen groups. My simulation system contains a frozen group and several non-frozen groups. Now, I'm testing the effects of mass of frozen atom on non-frozen group dynamics. I compared two simulations - In one case, the frozen atom has finite-mass while in the other, the frozen atom has zero-mass. In both cases, the averaged velocities of non-frozen groups are different. Could anybody explain this happening? I would deeply appreciate any comment. Jae H. Park ======================================= Jae Hyun Park, Ph.D. Postdoctoral Associate 3221 Beckamn Institute University of Illinois at Urbana-Champaign 405 North Mathews Avenue Urbana, IL 61801 (Tel) 217-244-4353, (FAX) 217-244-4333 (E-mail) jaepark at uiuc.edu From melicher at cray.dbp.fmph.uniba.sk Wed Sep 13 13:10:14 2006 From: melicher at cray.dbp.fmph.uniba.sk (Milan Melichercik) Date: Wed, 13 Sep 2006 13:10:14 +0200 Subject: [gmx-users] Question about parallazing Gromacs In-Reply-To: <6a91f07b0609130342j5f2f5f8di482c48c9a0e9fb2d@mail.gmail.com> References: <6a91f07b0609130342j5f2f5f8di482c48c9a0e9fb2d@mail.gmail.com> Message-ID: <200609131310.15335.melicher@cray.dbp.fmph.uniba.sk> D?a St 13. September 2006 12:42 Qiao Baofu nap?sal: > Hi all, > > I have a question about parallazing gromacs: I run the same system on a > cluster of my institute and my local computer, > Cluster:* *dual processor boards AMD Opteron 270 (Dual-Core), 2.0 GHz > Local computer: AMD X86-64 Cpu, double precision > > 1. The cluster (nodes=3:ppn=4) runs 87950 MD steps for one hour > 2. The cluster (nodes=5:ppn=4) runs 42749 MD steps for one hour > 3. The cluster (nodes=11:ppn=4) runs 5962 MD steps for one hour > 3. My local computer runs 179090 MD steps For 1hour 51 mintues. > > It is verry strange that the more cpus I use, the slowest the gromacs > runs.!! > > Who knows what's wrong with my job? And for paralleled gromacs, how many > cpus is prefered? As far as I know, the problem isn't your job but the interconnet between nodes, cause MD (and many other paralel computations) are very sensitive to the interconnect (network) bandwith and even more to the latencies - the processes need to transfer large amount of data to the other nodes and till the other nodes don't have them, they cannot compute. The other problem can be related with the congestion of the network, so the switch (or generally network) isn't able to transfer so large amount of data and throw away some of them... So (in the extreme case of the very slow net) you will have the fastest system by using only one node (and all of available CPU cores on it). I can't give you more specific answer cause I don't know your cluster. But the best result, I think, you can have simply by try the job on 1, 2, 3, etc. nodes... Milan Melichercik From qiaobf at gmail.com Wed Sep 13 14:03:04 2006 From: qiaobf at gmail.com (Qiao Baofu) Date: Wed, 13 Sep 2006 14:03:04 +0200 Subject: [gmx-users] how to write a annealing .mdp In-Reply-To: <450795FF.000026.28970@bj163app52.163.com> References: <450795FF.000026.28970@bj163app52.163.com> Message-ID: <6a91f07b0609130503g61293815u85591e6cf387a8f@mail.gmail.com> Hi, set T_couple=no and refer to the following script ; SIMULATED ANNEALING ; Type of annealing for each temperature group (no/single/periodic) annealing = single ; Number of time points to use for specifying annealing in each group annealing_npoints = 6 ; List of times at the annealing points for each group annealing_time = 0 10 20 30 40 50 ; Temp. at each annealing point, for each group. annealing_temp = 425 375 325 275 245 203 ?06-9-13?zzhwise1 ??? > > hello everyone > i want to anneal my system,but i don't konw how to wrote a right > annealing-mdp! > could anyone give me a moldel? > tanks in advaced! > > > > > > > > > > > > > > > 3G ? ? ? ? ??? ? ? ? ? ? ? ? ? ? > ? ? ? ? ? 3G ? ? ? ? ? ? ?280 ? ? ? ? ? ? ? ? ? ? ? ? ? > > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- Sincerely yours, ********************************************** Baofu Qiao, PhD Frankfurt Institute for Advanced Studies Max-von-Laue-Str. 1 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From Florian.Haberl at chemie.uni-erlangen.de Wed Sep 13 14:14:39 2006 From: Florian.Haberl at chemie.uni-erlangen.de (Florian Haberl) Date: Wed, 13 Sep 2006 14:14:39 +0200 Subject: [gmx-users] Question about parallazing Gromacs In-Reply-To: <200609131310.15335.melicher@cray.dbp.fmph.uniba.sk> References: <6a91f07b0609130342j5f2f5f8di482c48c9a0e9fb2d@mail.gmail.com> <200609131310.15335.melicher@cray.dbp.fmph.uniba.sk> Message-ID: <200609131414.41373.Florian.Haberl@chemie.uni-erlangen.de> hi, On Wednesday 13 September 2006 13:10, Milan Melichercik wrote: > D?a St 13. September 2006 12:42 Qiao Baofu nap?sal: > > Hi all, > > > > I have a question about parallazing gromacs: I run the same system on a > > cluster of my institute and my local computer, > > Cluster:* *dual processor boards AMD Opteron 270 (Dual-Core), 2.0 > > GHz Local computer: AMD X86-64 Cpu, double precision > > > > 1. The cluster (nodes=3:ppn=4) runs 87950 MD steps for one hour > > 2. The cluster (nodes=5:ppn=4) runs 42749 MD steps for one hour > > 3. The cluster (nodes=11:ppn=4) runs 5962 MD steps for one hour > > 3. My local computer runs 179090 MD steps For 1hour 51 mintues. > > > > It is verry strange that the more cpus I use, the slowest the gromacs > > runs.!! Try something like multiple of 2 not something like 10 nodes, you need also a fast interconnection like infiniband to reach a good scaling with a higher node number, but always use 2 4 8 cpus/cores. Upcoming release of gromacs will have a better scaling with new algos. You can try the cvs version with seperate pme nodes and domain decomposing. Gromacs 3.3.1 scales well with infiniband up to 32 cores. > > > > Who knows what's wrong with my job? And for paralleled gromacs, how > > many cpus is prefered? > > As far as I know, the problem isn't your job but the interconnet between > nodes, cause MD (and many other paralel computations) are very sensitive to > the interconnect (network) bandwith and even more to the latencies - the > processes need to transfer large amount of data to the other nodes and > till the other nodes don't have them, they cannot compute. The other > problem can be related with the congestion of the network, so the switch > (or generally network) isn't able to transfer so large amount of data and > throw away some of them... > So (in the extreme case of the very slow net) you will have the fastest > system by using only one node (and all of available CPU cores on it). I > can't give you more specific answer cause I don't know your cluster. But > the best result, I think, you can have simply by try the job on 1, 2, 3, > etc. nodes... > > Milan Melichercik > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Greetings, Florian -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) ? 9131 ? 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- From gmx3 at hotmail.com Wed Sep 13 14:46:17 2006 From: gmx3 at hotmail.com (Berk Hess) Date: Wed, 13 Sep 2006 14:46:17 +0200 Subject: [gmx-users] A method to scale Coulombic 1-4 interactions seperately In-Reply-To: <1158116925.4507763d418e9@webmail.utoronto.ca> Message-ID: >From: chris.neale at utoronto.ca >Reply-To: Discussion list for GROMACS users >To: gmx-users at gromacs.org >Subject: [gmx-users] A method to scale Coulombic 1-4 interactions >seperately >Date: Tue, 12 Sep 2006 23:08:45 -0400 > >There is a recent publication about combining the Berger lipids with >OPLS-AA and >getting the correct 1-4 scaling factor. New dihedrals were developed >because it >is possible to set special 1-4 parameters for LJ, but not coulomb. However, >there is another workaround to this that should be generally applicable to >1-4 >coulombic scaling. > >The lipids.itp file has already defined [ pairtypes ] so the LJ 1-4 is >scaled >correctly (FudgeLJ will not be applied to the values in [ pairtypes ]). The >problem now is that OPLS-AA requires a FudgeQQ of 0.5 and the Berger lipids >desire a FudgeQQ of one. > >The solution comes in two parts: >1. Divide the epsilon entries in the [ pairtypes ] of lipid.itp by 2.0. Now >the >LJ and coulombic 1-4 interactions are both exactly half of what they should >be. >2. Every entry in the [ pairs ] section of pope.itp should appear twice. >Now the >LJ and coulombic 1-4 interactions are both exactly what they should be. > >This solution should work for an arbitrary 1-4 scaling problem, just make >sure >that you get the ratios correct. A detailed method is outlined below and >that is >followed by the method that I used to test this procedure. I have also run >a >0.5ns simulation and the system "looks" fine (when I say looks fine I mean >by >visual inspection or by g_density). 0.5ns is not nearly long enough to >properly >evaluate area per lipid, but for what it's worth I get 0.53nm^2 per lipid >with >regular combination rules and 0.52nm^2 per lipid with the >half-epsilon-double-pair method outlined here. > >Perhaps the Gromacs crew could tell us whether a double [ pairs ] entry >might >run into problems in any special situations? No, there are no problems at all. A slightly cleaner method would be to leave the LJ pair parameters in the force field section unchanged and add the double pairs with additional 0 0 parameters for the LJ. Berk. From spoel at xray.bmc.uu.se Wed Sep 13 15:15:20 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Wed, 13 Sep 2006 06:15:20 -0700 Subject: [gmx-users] Question about parallazing Gromacs In-Reply-To: <6a91f07b0609130342j5f2f5f8di482c48c9a0e9fb2d@mail.gmail.com> References: <6a91f07b0609130342j5f2f5f8di482c48c9a0e9fb2d@mail.gmail.com> Message-ID: <45080468.9060000@xray.bmc.uu.se> Qiao Baofu wrote: > Hi all, > > I have a question about parallazing gromacs: I run the same system on a > cluster of my institute and my local computer, > Cluster:* * dual processor boards AMD Opteron 270 (Dual-Core), 2.0 GHz > Local computer: AMD X86-64 Cpu, double precision > > 1. The cluster (nodes=3:ppn=4) runs 87950 MD steps for one hour > 2. The cluster (nodes=5:ppn=4) runs 42749 MD steps for one hour > 3. The cluster (nodes=11:ppn=4) runs 5962 MD steps for one hour > 3. My local computer runs 179090 MD steps For 1hour 51 mintues. > > It is verry strange that the more cpus I use, the slowest the gromacs > runs.!! > > Who knows what's wrong with my job? And for paralleled gromacs, how > many cpus is prefered? > > > > The grompp command is: grompp -np 12 -o md3.mdp -c md3in.gro -p > MCl.top -o md3.tpr > > The following is one of the the job scripts on the cluster: > > # > # MD NTP(Berendsen&Berendsen, T=425&P=1bar),200ps tau_p=4 > # > # > #!/bin/bash > #PBS -N "md3" > # > #PBS -l walltime=01:00:00,nodes=3:ppn=4 > # > #PBS -m abe > # > #PBS -o md3.out > # > #PBS -e md3.err > # > # > cd /work/fias/qiao/time_checking/nodes3/ > /usr/local/Cluster-Apps/lam/gcc/64/7.1.1/bin/lamboot $PBS_NODEFILE > /usr/local/Cluster-Apps/lam/gcc/64/7.1.1/bin/mpirun -np 12 mdrun -v -s > md3.tpr -x md3 -e md3 -c md3 -g md3 > exit 0 > > > -- > Sincerely yours, > ********************************************** > Baofu Qiao, PhD > Frankfurt Institute for Advanced Studies > ********************************************** > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php try running on one quad node. gromacs 3.3 does not scale very well, we're working on improving that for 4.0. -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From wang at bioinformatik.uni-saarland.de Wed Sep 13 13:54:45 2006 From: wang at bioinformatik.uni-saarland.de (Wang Ling) Date: Wed, 13 Sep 2006 13:54:45 +0200 Subject: [gmx-users] about AFM pulling of one complex of two proteins Message-ID: <200609131354.45418.wang@bioinformatik.uni-saarland.de> hi, everyone now i am trying to pull one complex apart, which includes two proteins. but i met one problem, when i fixed the COM of one protein, pulling the COM of another protein, i found the pulled protein unfolding before pulling these two proteins apart, this is not the result i expected. my objective is to pull these two proteins apart, in order to study the interaction between two proteins. while the structures of these two proteins themselves don't change too much, could you give me some suggestions? i have read some references about AFM pulling, i found most of the papers are to pull a small molecule(no complicated secondary structures) from a big biological molecules, while in my case, the reference group and the pulled group are both complicated proteins, the interactions within the proteins and between the proteins are similiar, therefore before pulling the interface apart, the pulled group unfolding first. so i want to know if AFM pulling in Gromacs can do this kind of pulling? Thanks in advance! From cesar.araujo at oulu.fi Thu Sep 14 00:48:10 2006 From: cesar.araujo at oulu.fi (Cesar Araujo) Date: Wed, 13 Sep 2006 15:48:10 -0700 Subject: [gmx-users] Re: Question about parallazing Gromacs (Qiao Baofu) References: <20060913121511.A76112407D@xray.bmc.uu.se> Message-ID: <00dd01c6d786$b3683ba0$83e8e782@mole232131> Well, there is a common misconception with parallel computing. Usually, you will have an optimun number of processors that guarantees the best performance. More or less than that number will result in a decreased performance and longer computation times. The optimum number of processors will depend on the particular problem and the hardware/software configuration of your cluster, but for instance, in my case for docking experiments I've found that 4 cpu's is Ok. If I try to use more than 4 cpus the performance is worst. The same is for less than 4 cpu's. You have to find your optimum making some tests with your settings. To do that you can start your simulation and interrupt after a while to have some data logged in the log file. Then, from the information in that log file you can estimate the time that the whole task will take and compare using more or less number of processors until you find your optimum value. I hope it helps. Regards, C?sar.- > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 13 Sep 2006 12:42:37 +0200 > From: "Qiao Baofu" > Subject: [gmx-users] Question about parallazing Gromacs > To: gmx-users at gromacs.org > Message-ID: > <6a91f07b0609130342j5f2f5f8di482c48c9a0e9fb2d at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi all, > > I have a question about parallazing gromacs: I run the same system on a > cluster of my institute and my local computer, > Cluster:* *dual processor boards AMD Opteron 270 (Dual-Core), 2.0 GHz > Local computer: AMD X86-64 Cpu, double precision > > 1. The cluster (nodes=3:ppn=4) runs 87950 MD steps for one hour > 2. The cluster (nodes=5:ppn=4) runs 42749 MD steps for one hour > 3. The cluster (nodes=11:ppn=4) runs 5962 MD steps for one hour > 3. My local computer runs 179090 MD steps For 1hour 51 mintues. > > It is verry strange that the more cpus I use, the slowest the gromacs > runs.!! > > Who knows what's wrong with my job? And for paralleled gromacs, how many > cpus is prefered? > > > > The grompp command is: grompp -np 12 -o md3.mdp -c md3in.gro -p > MCl.top -o > md3.tpr > > The following is one of the the job scripts on the cluster: > > # > # MD NTP(Berendsen&Berendsen, T=425&P=1bar),200ps tau_p=4 > # > # > #!/bin/bash > #PBS -N "md3" > # > #PBS -l walltime=01:00:00,nodes=3:ppn=4 > # > #PBS -m abe > # > #PBS -o md3.out > # > #PBS -e md3.err > # > # > cd /work/fias/qiao/time_checking/nodes3/ > /usr/local/Cluster-Apps/lam/gcc/64/7.1.1/bin/lamboot $PBS_NODEFILE > /usr/local/Cluster-Apps/lam/gcc/64/7.1.1/bin/mpirun -np 12 mdrun -v -s > md3.tpr -x md3 -e md3 -c md3 -g md3 > exit 0 > > > -- > Sincerely yours, > ********************************************** > Baofu Qiao, PhD > Frankfurt Institute for Advanced Studies > ********************************************** > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20060913/fdee271a/attachment-0001.html > From Mikko.Hellgren at ki.se Wed Sep 13 16:09:55 2006 From: Mikko.Hellgren at ki.se (Mikko Hellgren) Date: Wed, 13 Sep 2006 16:09:55 +0200 Subject: [gmx-users] g_lie restraints, neutral ?? Message-ID: Hi MD people! Some questions about g_lie..... My purpose is to score different ligands and get a rough estimation of the free energy of binding between free and bound state of the ligands and protein of interest. 1. When I run my ligands in water without the protein, should I add counterions (Cl and Na) to make the system neutral. 2. Should I put any restraints on the ligand in the simulation without the protein? 3. When I run my ligand bound to the protein. Should I put restraints any restrains on protein or ligand My initial thought would be to put restraints on c-alpha of the protein and let the rest of the system be "free". Thank you for any suggestions or comments, by the way I have checked all previous threads with g_lie or lie without any to me clear suggestions about these questions. Take care, Mikko -------------- next part -------------- A non-text attachment was scrubbed... Name: mikhel.vcf Type: text/x-vcard Size: 343 bytes Desc: Card for Mikko Hellgren URL: From dmobley at gmail.com Wed Sep 13 17:00:23 2006 From: dmobley at gmail.com (David Mobley) Date: Wed, 13 Sep 2006 08:00:23 -0700 Subject: [gmx-users] Question about frozen group: In-Reply-To: <20060913055606.ABT20392@expms1.cites.uiuc.edu> References: <20060913055606.ABT20392@expms1.cites.uiuc.edu> Message-ID: Is the difference statistically significant? That is, if you even ran the *same* trajectory a couple times you would get slightly different average velocities. On 9/13/06, Jae Hyun Park wrote: > Hi, all GROMACS users: > > I have a simple question about frozen groups. My simulation system contains a frozen group and several non-frozen groups. Now, I'm testing the effects of mass of frozen atom on non-frozen group dynamics. I compared two simulations - In one case, the frozen atom has finite-mass while in the other, the frozen atom has zero-mass. In both cases, the averaged velocities of non-frozen groups are different. > > Could anybody explain this happening? I would deeply appreciate any comment. > > Jae H. Park > ======================================= > Jae Hyun Park, Ph.D. > Postdoctoral Associate > 3221 Beckamn Institute > University of Illinois at Urbana-Champaign > 405 North Mathews Avenue > Urbana, IL 61801 > (Tel) 217-244-4353, (FAX) 217-244-4333 > (E-mail) jaepark at uiuc.edu > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > From dmobley at gmail.com Wed Sep 13 17:09:45 2006 From: dmobley at gmail.com (David Mobley) Date: Wed, 13 Sep 2006 08:09:45 -0700 Subject: [gmx-users] wham question In-Reply-To: <20060913033149.78506.qmail@web51002.mail.yahoo.com> References: <20060913015304.023EC2407E@xray.bmc.uu.se> <20060913033149.78506.qmail@web51002.mail.yahoo.com> Message-ID: Manohar, I don't have a tutorial, but have done a bit of this. I think GROMACS has some built in tools for WHAM, but I have never used these. I just apply harmonic restraints to pull a ligand out of the binding site and then use my own WHAM code to analyze the data. In terms of picking the number of umbrellas and the spring constants, there are semi-automated or adaptive ways to do this, but none that are implemented in GROMACS, I think. So my approach so far has been to specify a set of umbrella centers and spring constants, then run some fairly short (i.e. 100 ps) trajectories and look at the resulting distance distributions. You want to make sure you get good overlap. Usually it takes some iteration before you get to the point where you have enough umbrellas, centered at the right places, with the right spring constants, in order to ensure good overlap. This, however, is key -- without good overlap, you'll get an answer, but it will be wrong (or, if you're lucky/unlucky, depending on your perspective, right for the wrong reason). After I find something that gives me reasonable-looking overlap for short trajectories, then I go ahead and run longer "production" simulations before doing the analysis. The additional complication is how exactly you pull the ligand out of a binding site. You might want to look at the PNAS paper by Woo and Roux (102:6825-6830) for an example. One issue is that if you just pull the ligand with simple distance restraints, there is no guarantee that you will pull it in a sane direction. This also may be especially problematic when the ligand begins leaving the protein, as at any fixed distance from a reference atom in the protein, it will be able to sample everywhere on a spherical shell, which can take a long time to equilibrate. My approach so far has been to try and use cartesian restraints to pull the ligand out along a particular axis that I specify in advance, and then compute the free energy of turning off the cartesian restraints at the endpoints. I'm not sure that this will work, yet, but at least it gets around the problems I just described. I'm not sure how Woo and Roux got around this; it sounds like they pulled along a particular axis; perhaps the ability to do that is implemented in CHARMM. You might be able to also do this by using an appropriate combination of distance and angle restraints between some atoms in the protein and ligand, in order to specify a direction. To make a long story short: I don't have a silver bullet, sorry. David On 9/12/06, Manohar Murthi wrote: > hi all > > does anyone have an example/tutorial of how to do > umbrella sampling using gromacs & wham? > > i'm about to try to calculate free energies of binding > using this method. > > i can find no information whatsoever about 'wham.gct', > which is an optional input mentioned in the mdrun > online reference page. what is this file supposed to > contain? > > i've yet to actually try it, but setting up the other > input files seems relatively straightforward. > > i'm hoping to benefit from others' experience to > figure out how to choose and vary the harmonic force > constants for the different umbrella runs. > > any advice would be greatly appreciated. > > cheers > mo > > > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > From dmobley at gmail.com Wed Sep 13 17:13:20 2006 From: dmobley at gmail.com (David Mobley) Date: Wed, 13 Sep 2006 08:13:20 -0700 Subject: SV: Re: [gmx-users] constraint distance In-Reply-To: <20060911134737.81658.qmail@web27409.mail.ukl.yahoo.com> References: <450559FA.30900@xray.bmc.uu.se> <20060911134737.81658.qmail@web27409.mail.ukl.yahoo.com> Message-ID: Allow me to take this opportunity to reiterate that the ability to only apply distance/angle/dihedral restraints between atoms in the same "molecule" (in the topology sense) is really lame. It would be really nice if GROMACS could handle absolute atom numbering for restraints (i.e. using the numbering as in the .gro file rather than in the topology file). David On 9/11/06, Soren Enemark wrote: > > > David van der Spoel skrev: > Soren Enemark wrote: > > Hi, > > maybe I am misunderstanding either the manual or the topic.. but - in > > my world - > > I never stop being puzzled by the part of chapt 6 in the manual which > > apparently > > says that such distance constraining is possible even though it (seems) > > to be > > secretly known that it is _not_ possible unless one uses the method > > suggested > > below. > > I believe, I suggest adding a comment in the manual. > > > > can you be more specific which part of the manual you mean? > > Basically almost anywhere in chapter 6 from 6.1 to 6.25 included. > > I mean, pulling works between 2 different molecules, why is it then obvious > that constraining doesn't? > > > > > -Soren > > > > */Tsjerk Wassenaar /* skrev: > > > > > Hi Kanin, > > > > The only way to get away with that is to merge your two parts to form > > one molecule, with the only connection being a distance_restraint (or > > another bonded term if you want to emulate bond-like behaviour such as > > a salt-bridge). > > > > Best, > > > > Tsjerk > > > > On 9/11/06, kanin wichapong wrote: > > > Dear All > > > I would like to know how to constraint the distance between the > > > different molecule, ex. the ligand and the protein. As far as I know > > > whatever to do the constraint, distance, angle dihedral, it can > > do just in > > > the same molecule. > > > Thank you in advance for all of your help. > > > > > > With Best all regard, > > > Kanin > > > > > > _______________________________________________ > > > gmx-users mailing list gmx-users at gromacs.org > > > http://www.gromacs.org/mailman/listinfo/gmx-users > > > Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to gmx-users-request at gromacs.org. > > > Can't post? Read > > > http://www.gromacs.org/mailing_lists/users.php > > > > > > > > > > > > -- > > > > Tsjerk A. Wassenaar, M.Sc. > > Groningen Biomolecular Sciences and Biotechnology Institute (GBB) > > Dept. of Biophysical Chemistry > > University of Groningen > > Nijenborgh 4 > > 9747AG Groningen, The Netherlands > > +31 50 363 4336 > > _______________________________________________ > > gmx-users mailing list gmx-users at gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-request at gromacs.org. > > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users mailing list gmx-users at gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-request at gromacs.org. > > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > From dmobley at gmail.com Wed Sep 13 17:15:08 2006 From: dmobley at gmail.com (David Mobley) Date: Wed, 13 Sep 2006 08:15:08 -0700 Subject: [gmx-users] constraint distance between ligand and protein In-Reply-To: <172bb8a80609110836w2beb8e67s8105e3982311c2b3@mail.gmail.com> References: <172bb8a80609110836w2beb8e67s8105e3982311c2b3@mail.gmail.com> Message-ID: Kanin, On 9/11/06, kanin wichapong wrote: > Hi All, > I would like to know how to make a distance constraint between the > ligand and the protein. If I just merge two chain together by pdb2gmx, it > can done if the two chain are both protein. However, if it is a ligand and > protein, i can't merge together because there is no libraly for the ligand > force field and then it can't generate the .itp or .top file You need a script to do this, as there's no built-in way to do it. I'm assuming you DO already have top and gro files for the ligand, though? If so, I have a script I use to do this for my ligand/proteins... With a bit of modification you could probably make it work for you. E-mail me off list if interested. David > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > From fefan at utmb.edu Wed Sep 13 19:33:06 2006 From: fefan at utmb.edu (Fan, Fenghui ) Date: Wed, 13 Sep 2006 12:33:06 -0500 Subject: [gmx-users] Intial velocity Message-ID: Dear all, For MD we need to get a initial velocity of the molecule randomly. Id the velocity linear vvelocity of the whole molecule or the vibration velovcity or some kinds of other velocity? In addition, as for the molecule is very large, there is the possibility that differeny parts of the protein has different velocity. Does this violate the randomly got velocity? Further more, for the MD system. it is in fact protein (can include ions and ligands) surrounded by water. Then it seems there will be no linaear movement of the whole molecule. I am looking forward to having these clarified. Best regards. Fenghui Fan From svb1 at msstate.edu Wed Sep 13 19:41:21 2006 From: svb1 at msstate.edu (svb1 at msstate.edu) Date: Wed, 13 Sep 2006 12:41:21 -0500 Subject: [gmx-users] Fatal error: Force field inconsistency In-Reply-To: <1158091046.45071127025ef@webmail.msstate.edu> References: <1158091046.45071127025ef@webmail.msstate.edu> Message-ID: <1158169281.450842c1c0758@webmail.msstate.edu> Quoting svb1 at msstate.edu: > > > Hello, > I had this error while trying to run a simulation for a small molecule > without > water and bilayer, I have included in the topol.top its parameters taken from > OPLS and its topology, since I did not created the topology with the pdb2gmx > I > did not included the ffoplsa.itp in the topol, however after grompp -norenum > ?debug, and mdrun I got the following message > Fatal error: Force field inconsistency: 1-4 interaction parameters for > atoms 9-10 not the same as for other atoms with the same atom type. > I already checked the [pairs] and found that for the same type of atoms the > parameters are the same . so why is giving me this error?. It doesn't make > sense. > I read in the GROMACS mailing list that including -norenum with grompp, it > make > work but it did not, so what I did was to commented out the 9-10 pair > interaction from [pairs], but still the same error, then I comented out > [pairs] > and all the 1-4 interactions defined in [pairs] in my molecule.itp, and after > grompp and mdrun the system did not complain. > The thing is that now it is calculating the 1-4 interactions from the > molecule > parameters in molecule.itp [which has the parameters and topology], with :[ > defaults ] > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ > 1 1 yes 1.0 0.5 > > because the explicit [pairs ] were comented out due to the Fatal error: Force > field inconsistency. > Can somebody give an advice, some people had this problem posted on the web, > but > I couldn't find the solution for my eventhought we all get the same error. > Thanks, > Sandra > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > From fefan at utmb.edu Wed Sep 13 19:24:44 2006 From: fefan at utmb.edu (Fan, Fenghui ) Date: Wed, 13 Sep 2006 12:24:44 -0500 Subject: [gmx-users] on restricted MD Message-ID: Dear all, I am now using gromacs to run a md of protein-ligand complex. I have already minimized the protein-ligand energy, and I try do run the protein restricted MD which allows the movement of ligand and water with tine 20 ps. However during the restriction MD, there is warnings showing that the bonds rotate more than 30 degree. Why this can happen? Does this violate thge meaning of restricted MD? In addition, for the coordinates, there is values extremely large, thus lead to the restricted process seems dead. Furthermore, there is some kinds of message like that: t=0.038 ps: water molecules starting at atom 4065 cannot be settled. WHy this can happen? In general, how to solve the above mentioned problems? I am looking forward to getting your reply. Best regards. Fenghui Fan From alokjain at iitk.ac.in Wed Sep 13 20:47:50 2006 From: alokjain at iitk.ac.in (alokjain at iitk.ac.in) Date: Thu, 14 Sep 2006 00:17:50 +0530 (IST) Subject: [gmx-users] re: RB dihedral potential query in OPLS In-Reply-To: <1158083082.4506f20ae9fda@webmail.utoronto.ca> References: <1158083082.4506f20ae9fda@webmail.utoronto.ca> Message-ID: <47315.172.28.124.187.1158173270.squirrel@newwebmail.iitk.ac.in> hello chris, thnks for your mail.So I just want to summarize our discusion over the last few mails...please tell me if i am correct. "When using OPLS-AA force field for simulation in GROMACS,it's correct to get a 14 energy term (Scaled) in addition to the RB potential". Ok so if that's the case can you please tell me in which case should i actually expect exclusion of the 14 interaction term when using RB potential???? Finally can you suggest a good reference on the RB potential. Thank you again. Regards. Alok Jain > Those OPLS-AA "Ryckaert Bellemans" terms are intended to work with [ pairs > ]. > They are not the same as the real RB terms. Here is a good explaination: > > http://www.gromacs.org/pipermail/gmx-users/2004-May/010500.html > > "The original Ryckaert Bellemans > potential is for carbon tails only (e.g. decane, or lipids). The same > potential is used in OPLS but with different parameters in which the > (scaled) pair interaction is part of the parameterization." > > My appologies for leading you astray earlier, I thought you were refering > to RB > terms in lipid tails. > > Chris. > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > From toma0052 at umn.edu Wed Sep 13 21:20:45 2006 From: toma0052 at umn.edu (toma0052) Date: Wed, 13 Sep 2006 14:20:45 CDT Subject: [gmx-users] Gromacs Surface tension Message-ID: <200609131920.k8DJKjj4011023@vendetta.software.umn.edu> Hi, I am not sure if this is how I should ask questions regarding Gromacs, but here goes. I was wondering if anyone knows if there is an internal program in Gromacs for calculating surface tension. I would like to model a lipid bilayer, and then determine the surface tension on that bilayer under certain conditions. Is there an included way for me to do that in Gromacs, or do I need to modify the Gromacs code? Thanks, Mike From paloureiro at biof.ufrj.br Wed Sep 13 22:12:18 2006 From: paloureiro at biof.ufrj.br (Pedro Alexandre Lapido Loureiro) Date: Wed, 13 Sep 2006 17:12:18 -0300 Subject: [gmx-users] Gromacs Surface tension In-Reply-To: <200609131920.k8DJKjj4011023@vendetta.software.umn.edu> References: <200609131920.k8DJKjj4011023@vendetta.software.umn.edu> Message-ID: <20060913171218.62xyfxq78y04cosg@webmail.biof.ufrj.br> > Hi, > I am not sure if this is how I should ask questions regarding Gromacs, > but here goes. I was wondering if anyone knows if there is an internal > program in Gromacs for calculating surface tension. I would like to model > a lipid bilayer, and then determine the surface tension on that bilayer > under certain conditions. Is there an included way for me to do that in > Gromacs, or do I need to modify the Gromacs code? > > Thanks, > Mike > Use the option "#Surf*SurfTens" in g_energy. Cheers. Pedro. ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From carlosjn at ce.fis.unam.mx Wed Sep 13 22:32:59 2006 From: carlosjn at ce.fis.unam.mx (=?ISO-8859-1?Q?Carlos_Javier_Nu=F1ez_Aguero?=) Date: Wed, 13 Sep 2006 15:32:59 -0500 Subject: [gmx-users] problems in installing fftw-3.0.1 under cygwin Message-ID: <45086AFB.9070102@ce.fis.unam.mx> Hi gmx-users, I am trying to install gmx-3.3.1 in my laptop (os windows xp & cygwin). Unfortunately, I didn't succeed to reproduce the instructions given by Mark Abraham in April-06. In my first attempt I uninstall (erroneously?) the fftw3 & fftw3-dev packages using the Cygwin installer. When I unpack the fftw-3.0.1.tar.gz file and run the command ./configure --enable-threads --enable-sse --enable-float the fftw-3.0.1 installation stop with the error: [...] checking for g77 ... g77 checking whether we are using the GNU fortran 77 compiler... yes checking whether g77 accepts -g.... yes checking how to get verbose linking output from g77... 39496 [unknown (0x5734)] g77 (21360) C:\cygwin\bin\g77.exe: *** fatal error - C:\cygwin\bin\g77.exe: ** * CreatedThread failed for sig - 0x0<0x0>, win32 error 1450 ./configure: line 15778: /usr/bin/grep: Resource temporarily unavailable 7 [unknown (0x540C)] grep (21512) C:\cygwin\bin\grep.exe: *** fatal error - C:\cygwin\bin\grep.exe: *** CreateThread failed for sig - 0x0<0x0>, win32 erro r 1450 7 [unlnown (0x5404)] sh (21504) C:\cygwin\bin\sh.exe: *** fatal error - C: \cygwin\bin\sh.exe: *** CreateThread failed for sig - 0x0<0x0>, Win32 error 1450 ./configure: line 15799: /usr/bin/grep: Resource temporarily unavailable 12 [main] sh 21632 fork: child -1 - CreateProcessA failed, errno 11 ./configure fork: Resource temporarily unavailable 8 [main] sh 21644 fork: child -1 -CreateProcessA failed, errno 11 18 [main] sh 6184 fork: child -1 - CreateProcessA failed, errno 11 ./configure: fork: Resource temporarily unavailable ./configure: line 15794: /usr/bin/cat: Resource temporarily unavailable 112196 [main] sh 6184 fork: child -1 - CreateProcessA failed, errno 11 ./configure: fork: Resource temporarily unavailable I do another attempt after re-install the fftw3 and fftw3-dev packages of the cygwin os. I un-install the fftw3 package (with cygwin installer), unpack the fftw-3.0.1.tar.gz and run the command ./configure --enable-threads .... the installation again stops now with the error: checking if more special flags are required for pthreads... no checking for cc_r... gcc configure: creating ./config.status config.status creating Makefile config.status: creating support/Makefile config.status: creating genfft/Makefile config.status: creatin genfft-k7/Makefile config.status: creating kernel/Makefile config.status: creating simd/Makefile config.status: creating dft/Makefile ./config.status: line 802: /usr/bin/sed: Resource temporarily unavailable ./config.status: line 802: /usr/bin/sed: Resource temporarily unavailable 13548 [main] sh 21568 fork: child -1 - CreateProcessA failed, errno 11 ./config.status: frk: Resouce temporarily unavailable config.status: creating dft/codelets/Makefile 16 [main] sh 21684 fork: child -1 - CreateProcessA failed, errno 11 ./config.status: fork: Resource temporarily unavailable 18 [main] sh 18348 fork: child -1 - CreateProcessA failed, errno 11 ./config.status: fork: Rsource temporarily unavailable 2076 [main] sh 18348 fork: child -1 - CreateProcessA failed, errno 11 ./config.status: fork: Resource temporarily unavailable ./config.status: line 802: /usr/bin/sed: Resource temporarily unavailable 25790 [main] sh 18348 fork: child -1 - CreateProcessA failed, errno 11 ./config.status: fork: Resource temporarily unavailable 28358 [main] sh 18348 fork: child -1 - CreateProcessA failed, errno 11 ./config.status: fork: Resource temporarily unavailable 10 [main] sh 21772 fork: child -1 - CreateProcessA failed, errno 11 ./config.status: fork: Resource temporarily unavailable 8 [main] sh 21820 fork: child -1 - CreateProcessA failed, errno 11 ./config.status: fork: Resource temporarily unavailable ./configure: line 18715: /usr/bin/sort: Resource temporarily unavailable ./configure: line 18734: /usr/bin/sort: Resource temporarily unavailable 19 [main] sh 2676 fork: child -1 - CreateProcessA failed, errno 11 ./configure: fork: resource temporarily unavailable 6169 [main] sh 2676 fork: child -1 - CreateProcessA failed, errno 11 ./configure: fork: Resource temporarily unavailable ./configure: line 18740: /usr/bin/sed: Resource temporarily unavailable Do you have idea on how to fix this problem? Thanks in advance, Regards, Javier Nu?ez -- No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.1.405 / Virus Database: 268.12.3/447 - Release Date: 9/13/2006 From chris.neale at utoronto.ca Thu Sep 14 01:16:27 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Wed, 13 Sep 2006 19:16:27 -0400 Subject: [gmx-users] re: RB dihedral potential query in OPLS Message-ID: <1158189387.4508914b298b0@webmail.utoronto.ca> >"When using OPLS-AA force field for simulation in GROMACS,it's correct to >get a 14 energy term (Scaled) in addition to the RB potential". It is correct to get the 14 energy term in addition to the RB potential. The 14 energy term will be affected by FudgeLJ/QQ if you use the 0.5/0.5 gen-pairs=yes as is intended for OPLS-AA... is this what you meant by "(scaled)"?. >Ok so if that's the case can you please tell me in which case should i >actually expect exclusion of the 14 interaction term when using RB >potential???? you should expect exclusion of 14 interaction terms when the RB potentials are parameterized for the removal of 14 interaction terms. This is probably limited to RB potentials in hydrocarbon chains (see references below). However, you must read the papers that published the parameters that you are using for the real answer to that question. Ryckaert and Bellemans. 1975 Molecular dynamics of liquid n-butane near its bioling point. Chem. Phys. Lett. 30:123-5 Ryckaert and Bellemans. 1978 Molecular dynamics of liquid alkanes. Faraday Discuss. Chem. Soc. 66:95-106 From chris.neale at utoronto.ca Thu Sep 14 01:54:25 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Wed, 13 Sep 2006 19:54:25 -0400 Subject: [gmx-users] A method to scale Coulombic 1-4 interactions seperately Message-ID: <1158191664.45089a310282f@webmail.utoronto.ca> >No, there are no problems at all. >A slightly cleaner method would be to leave the LJ pair parameters in >the force field section unchanged and add the double pairs >with additional 0 0 parameters for the LJ. Of course! That is a much better solution. From jhenin at vitae.cmm.upenn.edu Thu Sep 14 02:18:20 2006 From: jhenin at vitae.cmm.upenn.edu (Jerome Henin) Date: Wed, 13 Sep 2006 20:18:20 -0400 Subject: [gmx-users] about AFM pulling of one complex of two proteins In-Reply-To: <200609131354.45418.wang@bioinformatik.uni-saarland.de> References: <200609131354.45418.wang@bioinformatik.uni-saarland.de> Message-ID: <200609132018.20824.jhenin@cmm.upenn.edu> I would say one of these three statements holds (in order of increasing likelihood): 1) The force field does not describe the protein dimer accurately enough, 2) Your assumptions on the dissociation mechanism are wrong, 3) You are pulling too fast. Jerome On Wednesday 13 September 2006 07:54, Wang Ling wrote: > hi, everyone > > now i am trying to pull one complex apart, which includes two > proteins. but i met one problem, when i fixed the COM of one protein, > pulling the COM of another protein, i found the pulled protein unfolding > before pulling these two proteins apart, this is not the result i expected. > my objective is to pull these two proteins apart, in order to study the > interaction between two proteins. while the structures of these two > proteins themselves don't change too much, could you give me > some suggestions? > > i have read some references about AFM pulling, i found most of the > papers are to pull a small molecule(no complicated secondary structures) > from a big biological molecules, while in my case, the reference group and > the pulled group are both complicated proteins, the interactions within the > proteins and between the proteins are similiar, therefore before pulling > the interface apart, the pulled group unfolding first. so i want to know if > AFM pulling in Gromacs can do this kind of pulling? > > > Thanks in advance! > > > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- We don't need to worry about the Orwellian Big Brother any more -- the Internet has created a situation in which we need to worry about all of the Little Brothers out there instead. We have collectively become Big Brother. From spoel at xray.bmc.uu.se Thu Sep 14 03:19:28 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Wed, 13 Sep 2006 18:19:28 -0700 Subject: [gmx-users] Gromacs Surface tension In-Reply-To: <20060913171218.62xyfxq78y04cosg@webmail.biof.ufrj.br> References: <200609131920.k8DJKjj4011023@vendetta.software.umn.edu> <20060913171218.62xyfxq78y04cosg@webmail.biof.ufrj.br> Message-ID: <4508AE20.2080002@xray.bmc.uu.se> Pedro Alexandre Lapido Loureiro wrote: > > > >> Hi, >> I am not sure if this is how I should ask questions regarding >> Gromacs, >> but here goes. I was wondering if anyone knows if there is an internal >> program in Gromacs for calculating surface tension. I would like to >> model >> a lipid bilayer, and then determine the surface tension on that bilayer >> under certain conditions. Is there an included way for me to do that in >> Gromacs, or do I need to modify the Gromacs code? >> >> Thanks, >> Mike >> > > Use the option "#Surf*SurfTens" in g_energy. > and divide by two because you have two surfaces. > Cheers. > > Pedro. > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use thewww > interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From wilfred at sdsc.edu Thu Sep 14 03:02:28 2006 From: wilfred at sdsc.edu (Wilfred Li) Date: Wed, 13 Sep 2006 18:02:28 -0700 Subject: [gmx-users] problems in installing fftw-3.0.1 under cygwin In-Reply-To: <45086AFB.9070102@ce.fis.unam.mx> Message-ID: <452F37AE49199D49B1702D7D45038C4D744DD5@et.ad.sdsc.edu> Hi, You might be better off installing your own fftw (3.1.2 from http://www.fftw.org). Some people have reported that the "Resources unavailable" error may be due to some conflicts between Cygwin and other software/drivers such as web cams on Windows XP. Sometimes rebooting the machine helps. I did compile gmx 3.3.1 on XP, but didn't see this problem. Regards, Wilfred -----Original Message----- From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Carlos Javier Nu?ez Aguero Sent: Wednesday, September 13, 2006 1:33 PM To: gmx-users at gromacs.org Subject: [gmx-users] problems in installing fftw-3.0.1 under cygwin Hi gmx-users, I am trying to install gmx-3.3.1 in my laptop (os windows xp & cygwin). Unfortunately, I didn't succeed to reproduce the instructions given by Mark Abraham in April-06. In my first attempt I uninstall (erroneously?) the fftw3 & fftw3-dev packages using the Cygwin installer. When I unpack the fftw-3.0.1.tar.gz file and run the command ./configure --enable-threads --enable-sse --enable-float the fftw-3.0.1 installation stop with the error: [...] checking for g77 ... g77 checking whether we are using the GNU fortran 77 compiler... yes checking whether g77 accepts -g.... yes checking how to get verbose linking output from g77... 39496 [unknown (0x5734)] g77 (21360) C:\cygwin\bin\g77.exe: *** fatal error - C:\cygwin\bin\g77.exe: ** * CreatedThread failed for sig - 0x0<0x0>, win32 error 1450 ./configure: line 15778: /usr/bin/grep: Resource temporarily unavailable 7 [unknown (0x540C)] grep (21512) C:\cygwin\bin\grep.exe: *** fatal error - C:\cygwin\bin\grep.exe: *** CreateThread failed for sig - 0x0<0x0>, win32 erro r 1450 7 [unlnown (0x5404)] sh (21504) C:\cygwin\bin\sh.exe: *** fatal error - C: \cygwin\bin\sh.exe: *** CreateThread failed for sig - 0x0<0x0>, Win32 error 1450 ./configure: line 15799: /usr/bin/grep: Resource temporarily unavailable 12 [main] sh 21632 fork: child -1 - CreateProcessA failed, errno 11 ./configure fork: Resource temporarily unavailable 8 [main] sh 21644 fork: child -1 -CreateProcessA failed, errno 11 18 [main] sh 6184 fork: child -1 - CreateProcessA failed, errno 11 ./configure: fork: Resource temporarily unavailable ./configure: line 15794: /usr/bin/cat: Resource temporarily unavailable 112196 [main] sh 6184 fork: child -1 - CreateProcessA failed, errno 11 ./configure: fork: Resource temporarily unavailable I do another attempt after re-install the fftw3 and fftw3-dev packages of the cygwin os. I un-install the fftw3 package (with cygwin installer), unpack the fftw-3.0.1.tar.gz and run the command ./configure --enable-threads .... the installation again stops now with the error: checking if more special flags are required for pthreads... no checking for cc_r... gcc configure: creating ./config.status config.status creating Makefile config.status: creating support/Makefile config.status: creating genfft/Makefile config.status: creatin genfft-k7/Makefile config.status: creating kernel/Makefile config.status: creating simd/Makefile config.status: creating dft/Makefile ./config.status: line 802: /usr/bin/sed: Resource temporarily unavailable ./config.status: line 802: /usr/bin/sed: Resource temporarily unavailable 13548 [main] sh 21568 fork: child -1 - CreateProcessA failed, errno 11 ./config.status: frk: Resouce temporarily unavailable config.status: creating dft/codelets/Makefile 16 [main] sh 21684 fork: child -1 - CreateProcessA failed, errno 11 ./config.status: fork: Resource temporarily unavailable 18 [main] sh 18348 fork: child -1 - CreateProcessA failed, errno 11 ./config.status: fork: Rsource temporarily unavailable 2076 [main] sh 18348 fork: child -1 - CreateProcessA failed, errno 11 ./config.status: fork: Resource temporarily unavailable ./config.status: line 802: /usr/bin/sed: Resource temporarily unavailable 25790 [main] sh 18348 fork: child -1 - CreateProcessA failed, errno 11 ./config.status: fork: Resource temporarily unavailable 28358 [main] sh 18348 fork: child -1 - CreateProcessA failed, errno 11 ./config.status: fork: Resource temporarily unavailable 10 [main] sh 21772 fork: child -1 - CreateProcessA failed, errno 11 ./config.status: fork: Resource temporarily unavailable 8 [main] sh 21820 fork: child -1 - CreateProcessA failed, errno 11 ./config.status: fork: Resource temporarily unavailable ./configure: line 18715: /usr/bin/sort: Resource temporarily unavailable ./configure: line 18734: /usr/bin/sort: Resource temporarily unavailable 19 [main] sh 2676 fork: child -1 - CreateProcessA failed, errno 11 ./configure: fork: resource temporarily unavailable 6169 [main] sh 2676 fork: child -1 - CreateProcessA failed, errno 11 ./configure: fork: Resource temporarily unavailable ./configure: line 18740: /usr/bin/sed: Resource temporarily unavailable Do you have idea on how to fix this problem? Thanks in advance, Regards, Javier Nu?ez -- No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.1.405 / Virus Database: 268.12.3/447 - Release Date: 9/13/2006 _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php From spoel at xray.bmc.uu.se Thu Sep 14 03:28:34 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Wed, 13 Sep 2006 18:28:34 -0700 Subject: [gmx-users] Intial velocity In-Reply-To: References: Message-ID: <4508B042.4030006@xray.bmc.uu.se> Fan, Fenghui wrote: > Dear all, > > For MD we need to get a initial velocity of the molecule randomly. Id the velocity linear vvelocity of the whole molecule or the vibration velovcity or some kinds of other velocity? > > In addition, as for the molecule is very large, there is the possibility that differeny parts of the protein has different velocity. Does this violate the randomly got velocity? > > Further more, for the MD system. it is in fact protein (can include ions and ligands) surrounded by water. Then it seems there will be no linaear movement of the whole molecule. > > I am looking forward to having these clarified. > > Best regards. > > Fenghui Fan > > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php this is described in the manual. the velocities are sampled according to a Maxwell-Boltzmann distribution at the temperature you request. -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From mark.abraham at anu.edu.au Thu Sep 14 05:55:47 2006 From: mark.abraham at anu.edu.au (Mark Abraham) Date: Thu, 14 Sep 2006 13:55:47 +1000 (EST) Subject: [gmx-users] problems in installing fftw-3.0.1 under cygwin In-Reply-To: <45086AFB.9070102@ce.fis.unam.mx> References: <45086AFB.9070102@ce.fis.unam.mx> Message-ID: <42187.150.203.145.27.1158206147.squirrel@sqmail.anu.edu.au> > Hi gmx-users, > > I am trying to install gmx-3.3.1 in my laptop (os windows xp & cygwin). > Unfortunately, I didn't succeed > to reproduce the instructions given by Mark Abraham in April-06. > > In my first attempt I uninstall (erroneously?) the fftw3 & fftw3-dev > packages > using the Cygwin installer. When I unpack the fftw-3.0.1.tar.gz file and > run > the command > > ./configure --enable-threads --enable-sse --enable-float You can try without --enable-threads > g77 (21360) C:\cygwin\bin\g77.exe: *** fatal error - > C:\cygwin\bin\g77.exe: ** > ./config.status: line 802: /usr/bin/sed: Resource temporarily unavailable The kinds of errors you report seem to be a generic problem with your installation of cygwin. I think the shell from which you are running may have PATH problems, or you have a broken binutils package, or something similarly severe that hasn't got much to do with gromacs and fftw3. Try installing some other software (which uses configure) from source code to see if that is successful. If not, then I'd suggest re-installing compilers, binary utility packages and the like, and eventually, removing and re-installing Cygwin. Mark From mark.abraham at anu.edu.au Thu Sep 14 05:59:17 2006 From: mark.abraham at anu.edu.au (Mark Abraham) Date: Thu, 14 Sep 2006 13:59:17 +1000 (EST) Subject: [gmx-users] Re: Question about parallazing Gromacs (Qiao Baofu) In-Reply-To: <00dd01c6d786$b3683ba0$83e8e782@mole232131> References: <20060913121511.A76112407D@xray.bmc.uu.se> <00dd01c6d786$b3683ba0$83e8e782@mole232131> Message-ID: <43534.150.203.145.27.1158206357.squirrel@sqmail.anu.edu.au> > You have to > find your optimum making some tests with your settings. To do that you can > start your simulation and interrupt after a while to have some data logged > in the log file. Then, from the information in that log file you can > estimate the time that the whole task will take and compare using more or > less number of processors until you find your optimum value. Of course, that "while" should be at least of the order of several minutes. There is a set-up cost borne once at the start of the calculation which is not proportional to the length of the calculation, so you need to run long enough to get out of the time period during which it dominates the linear component. Mark From mark.abraham at anu.edu.au Thu Sep 14 06:04:39 2006 From: mark.abraham at anu.edu.au (Mark Abraham) Date: Thu, 14 Sep 2006 14:04:39 +1000 (EST) Subject: [gmx-users] on restricted MD In-Reply-To: References: Message-ID: <44632.150.203.145.27.1158206679.squirrel@sqmail.anu.edu.au> > Dear all, I am now using gromacs to run a md of protein-ligand complex. I > have already minimized the protein-ligand energy, and I try do run the > protein restricted MD which allows the movement of ligand and water with > tine 20 ps. However during the restriction MD, there is warnings showing > that the bonds rotate more than 30 degree. Why this can happen? Does this > violate thge meaning of restricted MD? In addition, for the coordinates, > there is values extremely large, thus lead to the restricted process seems > dead. > > Furthermore, there is some kinds of message like that: > > t=0.038 ps: water molecules starting at atom 4065 cannot be settled. WHy > this can happen? > > In general, how to solve the above mentioned problems? Try visualizing your trajectory. My guess is that your topology is probably broken and that seeing it break will guide you to fix it. Otherwise, minimize more rigorously, e.g. by minimizing after you solvate as well. Mark From chris.neale at utoronto.ca Thu Sep 14 06:20:03 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Thu, 14 Sep 2006 00:20:03 -0400 Subject: [gmx-users] openmpi Message-ID: <1158207603.4508d87383de6@webmail.utoronto.ca> Anyone using openmpi for parallel gromacs? If so, how to set the maximum short tcp length? I have tried some things unsuccessfully which are posted at the open mpi site: http://www.open-mpi.org/community/lists/users/2006/09/1864.php From spoel at xray.bmc.uu.se Thu Sep 14 06:26:20 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Wed, 13 Sep 2006 21:26:20 -0700 Subject: [gmx-users] openmpi In-Reply-To: <1158207603.4508d87383de6@webmail.utoronto.ca> References: <1158207603.4508d87383de6@webmail.utoronto.ca> Message-ID: <4508D9EC.20906@xray.bmc.uu.se> chris.neale at utoronto.ca wrote: > Anyone using openmpi for parallel gromacs? If so, how to set the maximum short > tcp length? I have tried some things unsuccessfully which are posted at the open > mpi site: > http://www.open-mpi.org/community/lists/users/2006/09/1864.php I tried it on my Mac, and I had so many problem (read crashes) that I went back to LAM. > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From carlosjn at ce.fis.unam.mx Thu Sep 14 06:10:15 2006 From: carlosjn at ce.fis.unam.mx (=?ISO-8859-1?Q?Carlos_Javier_Nu=F1ez_Aguero?=) Date: Wed, 13 Sep 2006 23:10:15 -0500 Subject: [gmx-users] problems in installing fftw-3.0.1 under cygwin In-Reply-To: <42187.150.203.145.27.1158206147.squirrel@sqmail.anu.edu.au> References: <45086AFB.9070102@ce.fis.unam.mx> <42187.150.203.145.27.1158206147.squirrel@sqmail.anu.edu.au> Message-ID: <4508D627.5050702@ce.fis.unam.mx> Hi, Wilfred and Mark, thank you very much for the tips and your time. Best regards, Javier Nu?ez -- No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.1.405 / Virus Database: 268.12.3/447 - Release Date: 9/13/2006 From qiaobf at gmail.com Thu Sep 14 09:27:45 2006 From: qiaobf at gmail.com (Qiao Baofu) Date: Thu, 14 Sep 2006 09:27:45 +0200 Subject: [gmx-users] Re: Question about parallazing Gromacs (Qiao Baofu) In-Reply-To: <43534.150.203.145.27.1158206357.squirrel@sqmail.anu.edu.au> References: <20060913121511.A76112407D@xray.bmc.uu.se> <00dd01c6d786$b3683ba0$83e8e782@mole232131> <43534.150.203.145.27.1158206357.squirrel@sqmail.anu.edu.au> Message-ID: <6a91f07b0609140027u68ac3085tb01120f19b854545@mail.gmail.com> Hi, Thanks. I have test different cpus. Our institute has two clusters: one is each node has 4 cpu (A), one is one node has only 1 cpu (B). I made different tests on the two clusters and my local computer using the same system. See the following result: A (For 1 hour) # of cpus ; MD steps 4 finished (200000steps for 26:21) 8 finished (200000steps for 40:57) 12 87950 20 42749 44 5962 !!!!! B (For 1 hour) # of cpu ; MD steps 1 156991 for 56:12 2 179820 3 200,000 for 54:20 4 200,000 for 51:12 c. Local(single cpu), 200000 steps For 1h52:38 One can see that 1. On cluster A, one nodes(4 cpu) is just as 4 times fast as my local computer. 2. More than one nodes will decrease the performancs the gromacs, 3. On cluster B, the more cpu used, the faster gromacs runs. But the difference of speed is not apparent. 4. Cluster B with 4 cpus is slow as half as that Cluster A with 1 node (4 cpus) I wonder if anyone can tell the bottlenack: the hardware on the cluster or gromacs? 2006/9/14, Mark Abraham : > > > You have to > > find your optimum making some tests with your settings. To do that you > can > > start your simulation and interrupt after a while to have some data > logged > > in the log file. Then, from the information in that log file you can > > estimate the time that the whole task will take and compare using more > or > > less number of processors until you find your optimum value. > > Of course, that "while" should be at least of the order of several > minutes. There is a set-up cost borne once at the start of the calculation > which is not proportional to the length of the calculation, so you need to > run long enough to get out of the time period during which it dominates > the linear component. > > Mark > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Sincerely yours, ********************************************** Baofu Qiao, PhD Frankfurt Institute for Advanced Studies ********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From Mark.Abraham at anu.edu.au Thu Sep 14 09:53:58 2006 From: Mark.Abraham at anu.edu.au (Mark Abraham) Date: Thu, 14 Sep 2006 17:53:58 +1000 Subject: [gmx-users] Re: Question about parallazing Gromacs (Qiao Baofu) In-Reply-To: <6a91f07b0609140027u68ac3085tb01120f19b854545@mail.gmail.com> References: <20060913121511.A76112407D@xray.bmc.uu.se> <00dd01c6d786$b3683ba0$83e8e782@mole232131> <43534.150.203.145.27.1158206357.squirrel@sqmail.anu.edu.au> <6a91f07b0609140027u68ac3085tb01120f19b854545@mail.gmail.com> Message-ID: <45090A96.3020307@anu.edu.au> Qiao Baofu wrote: > Hi, > > Thanks. I have test different cpus. Our institute has two clusters: one > is each node has 4 cpu (A), one is one node has only 1 cpu (B). I made > different tests on the two clusters and my local computer using the same > system. See the following result: > > A (For 1 hour) > # of cpus ; MD steps > 4 finished (200000steps for 26:21) > 8 finished (200000steps for 40:57) > 12 87950 > 20 42749 > 44 5962 !!!!! > B (For 1 hour) > # of cpu ; MD steps > 1 156991 for 56:12 > 2 179820 > 3 200,000 for 54:20 > 4 200,000 for 51:12 > c. Local(single cpu), 200000 steps For 1h52:38 > > One can see that > 1. On cluster A, one nodes(4 cpu) is just as 4 times fast as my local > computer. > 2. More than one nodes will decrease the performancs the gromacs, > 3. On cluster B, the more cpu used, the faster gromacs runs. But the > difference of speed is not apparent. > 4. Cluster B with 4 cpus is slow as half as that Cluster A with 1 node > (4 cpus) > > I wonder if anyone can tell the bottlenack: the hardware on the cluster > or gromacs? Probably your interconnects between nodes are using carrier pigeons or something :-) I expect that 1 cpu on machine A will require around four times as long as 1 4-cpu node, which you can presumably test for yourself. For next time, if you want to compare hardware like this, either use the same length of time or the same number of MD steps for all of your runs. Also when reporting runtimes, make it clear whether you are reporting walltime or some time * number_of_cpus, etc. :-) Mark From priyankaps4 at yahoo.com Thu Sep 14 11:21:29 2006 From: priyankaps4 at yahoo.com (priyanka srivastava) Date: Thu, 14 Sep 2006 02:21:29 -0700 (PDT) Subject: [gmx-users] g_order C code Message-ID: <20060914092129.56307.qmail@web39213.mail.mud.yahoo.com> Dear Gromacs users, Hie, I am calculating the order parameters for a bilayer patch using g_order analysis tool in gromacs version 3.3. I have a total of 48 elements in the patch and I want the order parameter value for each and every element i.e. a total of say 48 values for order parameter alongwith the average which g_order reports. I tried to fiddle with the code too and tried changing the following section as follows: /* average over frames */ for (i = 1; i < nr_tails; i++) { /* svmul(1.0/nr_frames, (*order)[i], (*order)[i]);*/ fprintf(stderr,"Atom %d Tensor: x=%g , y=%g, z=%g\n",i,(*order)(index[i])[XX], (*order)(index[i])[YY], (*order)(index[i])[ZZ]); and also: sprintf(buf,"Deuterium order parameters"); slOrd = xvgropen(cfile,buf, "Atom", "Scd"); for (i = 1; i < nr_tails; i++) { fprintf(ord,"%12d %12g %12g %12g\n", atom, order(index[i])[XX], order(index[i])[YY], order(index[i])[ZZ]); fprintf(slOrd,"%12d %12g\n", atom, -1 * (0.6667 * order(index[i])[XX] + 0.333 * order(index[i])[YY])); The problem is I am not sure if that is the right way of doing this. Please suggest me something. Also once these changes have been incorporated in the C program how do I generate the exe of g_order. Gcc gives many undefined errors. Please suggest me something, regards, Priyanka. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From Florian.Haberl at chemie.uni-erlangen.de Thu Sep 14 11:39:27 2006 From: Florian.Haberl at chemie.uni-erlangen.de (Florian Haberl) Date: Thu, 14 Sep 2006 11:39:27 +0200 Subject: [gmx-users] Re: Question about parallazing Gromacs (Qiao Baofu) In-Reply-To: <45090A96.3020307@anu.edu.au> References: <20060913121511.A76112407D@xray.bmc.uu.se> <6a91f07b0609140027u68ac3085tb01120f19b854545@mail.gmail.com> <45090A96.3020307@anu.edu.au> Message-ID: <200609141139.34891.Florian.Haberl@chemie.uni-erlangen.de> On Thursday 14 September 2006 09:53, Mark Abraham wrote: > Qiao Baofu wrote: > > Hi, > > > > Thanks. I have test different cpus. Our institute has two clusters: one > > is each node has 4 cpu (A), one is one node has only 1 cpu (B). I made > > different tests on the two clusters and my local computer using the same > > system. See the following result: > > > > A (For 1 hour) > > # of cpus ; MD steps > > 4 finished (200000steps for 26:21) > > 8 finished (200000steps for 40:57) > > 12 87950 > > 20 42749 > > 44 5962 !!!!! > > B (For 1 hour) > > # of cpu ; MD steps > > 1 156991 for 56:12 > > 2 179820 > > 3 200,000 for 54:20 > > 4 200,000 for 51:12 > > c. Local(single cpu), 200000 steps For 1h52:38 > > > > One can see that > > 1. On cluster A, one nodes(4 cpu) is just as 4 times fast as my local > > computer. > > 2. More than one nodes will decrease the performancs the gromacs, > > 3. On cluster B, the more cpu used, the faster gromacs runs. But the > > difference of speed is not apparent. > > 4. Cluster B with 4 cpus is slow as half as that Cluster A with 1 node > > (4 cpus) > > > > I wonder if anyone can tell the bottlenack: the hardware on the cluster > > or gromacs? > > Probably your interconnects between nodes are using carrier pigeons or > something :-) I expect that 1 cpu on machine A will require around four > times as long as 1 4-cpu node, which you can presumably test for yourself. > > For next time, if you want to compare hardware like this, either use the > same length of time or the same number of MD steps for all of your runs. > Also when reporting runtimes, make it clear whether you are reporting > walltime or some time * number_of_cpus, etc. :-) Search the mailing list i have post several times benchmark results for different systems with standard benchmark suite. http://www.gromacs.org/pipermail/gmx-developers/2006-January/001473.html > > Mark > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Greetings, Florian -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) ? 9131 ? 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- From cesar.araujo at oulu.fi Thu Sep 14 21:48:04 2006 From: cesar.araujo at oulu.fi (Cesar Araujo) Date: Thu, 14 Sep 2006 12:48:04 -0700 Subject: [gmx-users] Re: Re: Re: Question about parallazing Gromacs References: <20060914080101.CCB812407E@xray.bmc.uu.se> Message-ID: <000601c6d836$b48f94a0$83e8e782@mole232131> > ------------------------------ > > Message: 7 > Date: Thu, 14 Sep 2006 09:27:45 +0200 > From: "Qiao Baofu" > Subject: Re: [gmx-users] Re: Question about parallazing Gromacs (Qiao > Baofu) > To: "Discussion list for GROMACS users" > Message-ID: > <6a91f07b0609140027u68ac3085tb01120f19b854545 at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > Thanks. I have test different cpus. Our institute has two clusters: one is > each node has 4 cpu (A), one is one node has only 1 cpu (B). I made > different tests on the two clusters and my local computer using the same > system. See the following result: > > A (For 1 hour) > # of cpus ; MD steps > 4 finished (200000steps for 26:21) > 8 finished (200000steps for 40:57) > 12 87950 > 20 42749 > 44 5962 !!!!! > B (For 1 hour) > # of cpu ; MD steps > 1 156991 for 56:12 > 2 179820 > 3 200,000 for 54:20 > 4 200,000 for 51:12 > c. Local(single cpu), 200000 steps For 1h52:38 > > One can see that > 1. On cluster A, one nodes(4 cpu) is just as 4 times fast as my local > computer. > 2. More than one nodes will decrease the performancs the gromacs, > 3. On cluster B, the more cpu used, the faster gromacs runs. But the > difference of speed is not apparent. > 4. Cluster B with 4 cpus is slow as half as that Cluster A with 1 node (4 > cpus) > > I wonder if anyone can tell the bottlenack: the hardware on the cluster or > gromacs? > > Well, probably it is a combination of bottlenecks in both software and hardware. Both of them should be optimized to guarantee the best performance. From the hardware side the delays in inter-node communication across the network can be the reason. But also, it can be related with software issues related to the operating system and network configuration. I think that the first thing to do is work in cluster setup to achieve the best performance for your hardware configuration. In addition, take into account that inter-node communication between two CPU's inside the same machine should be faster than between two CPU's across the network. >From the software side (Gromacs) the algorithms should be optimized with regard to the parallel programming model. David said in a previous answer that they have detected some problems in the software implementation and they are working to solve that issue in the next version of Gromacs. Regards, ----------------------------------------------------------- Cesar Araujo, Lic. of Chemistry Department of Molecular Endocrynology Oulu University Hospital FIN-90029 OYS, OULU, FINLAND phone: +358 8 3155632 e-mail: cesar.araujo at oulu.fi From erikm at xray.bmc.uu.se Thu Sep 14 12:09:24 2006 From: erikm at xray.bmc.uu.se (Erik Marklund) Date: Thu, 14 Sep 2006 12:09:24 +0200 Subject: [gmx-users] g_order C code In-Reply-To: <20060914092129.56307.qmail@web39213.mail.mud.yahoo.com> References: <20060914092129.56307.qmail@web39213.mail.mud.yahoo.com> Message-ID: <1158228564.7364.57.camel@jorn.bmc.uu.se> On Thu, 2006-09-14 at 02:21 -0700, priyanka srivastava wrote: > Dear Gromacs users, > Hie, > > I am calculating the order parameters for a bilayer > patch using g_order analysis tool in gromacs version > 3.3. > > I have a total of 48 elements in the patch and I want > the order parameter value for each and every element > i.e. a total of say 48 values for order parameter > alongwith the average which g_order reports. > > I tried to fiddle with the code too and tried changing > the following section as follows: > > /* average over frames */ > for (i = 1; i < nr_tails; i++) { > /* svmul(1.0/nr_frames, (*order)[i], > (*order)[i]);*/ > fprintf(stderr,"Atom %d Tensor: x=%g , y=%g, > z=%g\n",i,(*order)(index[i])[XX], > (*order)(index[i])[YY], > (*order)(index[i])[ZZ]); > > > and also: > > sprintf(buf,"Deuterium order parameters"); > slOrd = xvgropen(cfile,buf, "Atom", "Scd"); > > for (i = 1; i < nr_tails; i++) { > fprintf(ord,"%12d %12g %12g %12g\n", atom, > order(index[i])[XX], > order(index[i])[YY], > order(index[i])[ZZ]); > fprintf(slOrd,"%12d %12g\n", atom, -1 * > (0.6667 * order(index[i])[XX] + > 0.333 > * order(index[i])[YY])); > > The problem is I am not sure if that is the right way > of doing this. Please suggest me something. Also once > these changes have been incorporated in the C program > how do I generate the exe of g_order. Gcc gives many > undefined errors. In src/tools: make g_order It may require that various libraries are already compiled, which is why you should build all of gromacs once too (in gmx: make install). Having done that once, make g_order should do the trick I think. > > Please suggest me something, > regards, > Priyanka. > > > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Erik Marklund, PhD Student, Molecular Biopcysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 erikm at xray.bmc.uu.se From qiaobf at gmail.com Thu Sep 14 12:28:47 2006 From: qiaobf at gmail.com (Qiao Baofu) Date: Thu, 14 Sep 2006 12:28:47 +0200 Subject: [gmx-users] Re: Re: Re: Question about parallazing Gromacs In-Reply-To: <000601c6d836$b48f94a0$83e8e782@mole232131> References: <20060914080101.CCB812407E@xray.bmc.uu.se> <000601c6d836$b48f94a0$83e8e782@mole232131> Message-ID: <6a91f07b0609140328k1d0ada4ela158f8d60d6fb9f6@mail.gmail.com> Thanks a lot! 2006/9/14, Cesar Araujo : > > > > ------------------------------ > > > > Message: 7 > > Date: Thu, 14 Sep 2006 09:27:45 +0200 > > From: "Qiao Baofu" > > Subject: Re: [gmx-users] Re: Question about parallazing Gromacs (Qiao > > Baofu) > > To: "Discussion list for GROMACS users" > > Message-ID: > > <6a91f07b0609140027u68ac3085tb01120f19b854545 at mail.gmail.com> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Hi, > > > > Thanks. I have test different cpus. Our institute has two clusters: one > is > > each node has 4 cpu (A), one is one node has only 1 cpu (B). I made > > different tests on the two clusters and my local computer using the same > > system. See the following result: > > > > A (For 1 hour) > > # of cpus ; MD steps > > 4 finished (200000steps for 26:21) > > 8 finished (200000steps for 40:57) > > 12 87950 > > 20 42749 > > 44 5962 !!!!! > > B (For 1 hour) > > # of cpu ; MD steps > > 1 156991 for 56:12 > > 2 179820 > > 3 200,000 for 54:20 > > 4 200,000 for 51:12 > > c. Local(single cpu), 200000 steps For 1h52:38 > > > > One can see that > > 1. On cluster A, one nodes(4 cpu) is just as 4 times fast as my local > > computer. > > 2. More than one nodes will decrease the performancs the gromacs, > > 3. On cluster B, the more cpu used, the faster gromacs runs. But the > > difference of speed is not apparent. > > 4. Cluster B with 4 cpus is slow as half as that Cluster A with 1 node > (4 > > cpus) > > > > I wonder if anyone can tell the bottlenack: the hardware on the cluster > or > > gromacs? > > > > > > Well, probably it is a combination of bottlenecks in both software and > hardware. > Both of them should be optimized to guarantee the best performance. From > the > hardware side the delays in inter-node communication across the network > can > be the reason. But also, it can be related with software issues related to > the operating > system and network configuration. I think that the first thing to do is > work > in cluster > setup to achieve the best performance for your hardware configuration. > > In addition, take into account that inter-node communication between two > CPU's > inside the same machine should be faster than between two CPU's across the > network. > > >From the software side (Gromacs) the algorithms should be optimized with > regard > to the parallel programming model. David said in a previous answer that > they > have detected some problems in the software implementation and they are > working > to solve that issue in the next version of Gromacs. > > Regards, > ----------------------------------------------------------- > Cesar Araujo, Lic. of Chemistry > Department of Molecular Endocrynology > Oulu University Hospital > FIN-90029 OYS, OULU, FINLAND > > phone: +358 8 3155632 > e-mail: cesar.araujo at oulu.fi > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Sincerely yours, ********************************************** Baofu Qiao, PhD Frankfurt Institute for Advanced Studies Max-von-Laue-Str. 1 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From qiaobf at gmail.com Thu Sep 14 12:45:07 2006 From: qiaobf at gmail.com (Qiao Baofu) Date: Thu, 14 Sep 2006 12:45:07 +0200 Subject: [gmx-users] Re: Question about parallazing Gromacs (Qiao Baofu) In-Reply-To: <45090A96.3020307@anu.edu.au> References: <20060913121511.A76112407D@xray.bmc.uu.se> <00dd01c6d786$b3683ba0$83e8e782@mole232131> <43534.150.203.145.27.1158206357.squirrel@sqmail.anu.edu.au> <6a91f07b0609140027u68ac3085tb01120f19b854545@mail.gmail.com> <45090A96.3020307@anu.edu.au> Message-ID: <6a91f07b0609140345va1e3436s37a4e896b5da8f14@mail.gmail.com> 2006/9/14, Mark Abraham : > > > Probably your interconnects between nodes are using carrier pigeons or > something :-) I expect that 1 cpu on machine A will require around four > times as long as 1 4-cpu node, which you can presumably test for yourself. It is forbidden to run only one cpu on the cluster A in my inisititute. For next time, if you want to compare hardware like this, either use the > same length of time or the same number of MD steps for all of your runs. > Also when reporting runtimes, make it clear whether you are reporting > walltime or some time * number_of_cpus, etc. :-) For all the jobs (except the one on my local computer) , I set walltime=1hour, and nsteps= 200,000,dt=0.001. The running time are taken from the end of the .log file. See the following example. NODE (s) Real (s) (%) Time: 1581.000 1581.000 100.0 26:21 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 56.376 4.515 10.930 2.196 Mark > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Sincerely yours, ********************************************** Baofu Qiao, PhD Frankfurt Institute for Advanced Studies Max-von-Laue-Str. 1 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From erikm at xray.bmc.uu.se Thu Sep 14 12:09:24 2006 From: erikm at xray.bmc.uu.se (Erik Marklund) Date: Thu, 14 Sep 2006 12:09:24 +0200 Subject: [gmx-users] g_order C code In-Reply-To: <20060914092129.56307.qmail@web39213.mail.mud.yahoo.com> References: <20060914092129.56307.qmail@web39213.mail.mud.yahoo.com> Message-ID: <1158228564.7364.57.camel@jorn.bmc.uu.se> On Thu, 2006-09-14 at 02:21 -0700, priyanka srivastava wrote: > Dear Gromacs users, > Hie, > > I am calculating the order parameters for a bilayer > patch using g_order analysis tool in gromacs version > 3.3. > > I have a total of 48 elements in the patch and I want > the order parameter value for each and every element > i.e. a total of say 48 values for order parameter > alongwith the average which g_order reports. > > I tried to fiddle with the code too and tried changing > the following section as follows: > > /* average over frames */ > for (i = 1; i < nr_tails; i++) { > /* svmul(1.0/nr_frames, (*order)[i], > (*order)[i]);*/ > fprintf(stderr,"Atom %d Tensor: x=%g , y=%g, > z=%g\n",i,(*order)(index[i])[XX], > (*order)(index[i])[YY], > (*order)(index[i])[ZZ]); > > > and also: > > sprintf(buf,"Deuterium order parameters"); > slOrd = xvgropen(cfile,buf, "Atom", "Scd"); > > for (i = 1; i < nr_tails; i++) { > fprintf(ord,"%12d %12g %12g %12g\n", atom, > order(index[i])[XX], > order(index[i])[YY], > order(index[i])[ZZ]); > fprintf(slOrd,"%12d %12g\n", atom, -1 * > (0.6667 * order(index[i])[XX] + > 0.333 > * order(index[i])[YY])); > > The problem is I am not sure if that is the right way > of doing this. Please suggest me something. Also once > these changes have been incorporated in the C program > how do I generate the exe of g_order. Gcc gives many > undefined errors. In src/tools: make g_order It may require that various libraries are already compiled, which is why you should build all of gromacs once too (in gmx: make install). Having done that once, make g_order should do the trick I think. > > Please suggest me something, > regards, > Priyanka. > > > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Erik Marklund, PhD Student, Molecular Biopcysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 erikm at xray.bmc.uu.se From priyankaps4 at yahoo.com Thu Sep 14 13:44:00 2006 From: priyankaps4 at yahoo.com (priyanka srivastava) Date: Thu, 14 Sep 2006 04:44:00 -0700 (PDT) Subject: [gmx-users] g_order C code In-Reply-To: <1158228564.7364.57.camel@jorn.bmc.uu.se> Message-ID: <20060914114400.46454.qmail@web39205.mail.mud.yahoo.com> Thank you for your reply. I am also curious to know if this is the right way of doing it. I am not sure of the changes that I have made in the code. Any suggestions on that please? Since, when I say "make install" it gives the following error: cc -DHAVE_CONFIG_H -I. -I. -I../../src -I/usr/X11R6/include -I../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -malign-double -funroll-all-loops -MT gmx_order.lo -MD -MP -MF .deps/gmx_order.Tpo -c gmx_order.c -o gmx_order.o gmx_order.c: In function `calc_order': gmx_order.c:251: called object is not a function gmx_order.c:252: called object is not a function gmx_order.c:252: called object is not a function gmx_order.c: In function `order_plot': gmx_order.c:300: `i' undeclared (first use in this function) gmx_order.c:300: (Each undeclared identifier is reported only once gmx_order.c:300: for each function it appears in.) gmx_order.c:301: called object is not a function gmx_order.c:302: called object is not a function gmx_order.c:302: called object is not a function gmx_order.c:303: called object is not a function gmx_order.c:304: called object is not a function make[2]: *** [gmx_order.lo] Error 1 make[2]: Leaving directory `/home/histidine/gromacs/gromacs-3.3/src/tools' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/home/histidine/gromacs/gromacs-3.3/src' make: *** [install-recursive] Error 1 thanks and regards, Priyanka. --- Erik Marklund wrote: > On Thu, 2006-09-14 at 02:21 -0700, priyanka > srivastava wrote: > > Dear Gromacs users, > > Hie, > > > > I am calculating the order parameters for a > bilayer > > patch using g_order analysis tool in gromacs > version > > 3.3. > > > > I have a total of 48 elements in the patch and I > want > > the order parameter value for each and every > element > > i.e. a total of say 48 values for order parameter > > alongwith the average which g_order reports. > > > > I tried to fiddle with the code too and tried > changing > > the following section as follows: > > > > /* average over frames */ > > for (i = 1; i < nr_tails; i++) { > > /* svmul(1.0/nr_frames, (*order)[i], > > (*order)[i]);*/ > > fprintf(stderr,"Atom %d Tensor: x=%g , y=%g, > > z=%g\n",i,(*order)(index[i])[XX], > > (*order)(index[i])[YY], > > (*order)(index[i])[ZZ]); > > > > > > and also: > > > > sprintf(buf,"Deuterium order parameters"); > > slOrd = xvgropen(cfile,buf, "Atom", "Scd"); > > > > for (i = 1; i < nr_tails; i++) { > > fprintf(ord,"%12d %12g %12g %12g\n", > atom, > > order(index[i])[XX], > > order(index[i])[YY], > > order(index[i])[ZZ]); > > fprintf(slOrd,"%12d %12g\n", atom, -1 * > > (0.6667 * order(index[i])[XX] + > > > 0.333 > > * order(index[i])[YY])); > > > > The problem is I am not sure if that is the right > way > > of doing this. Please suggest me something. Also > once > > these changes have been incorporated in the C > program > > how do I generate the exe of g_order. Gcc gives > many > > undefined errors. > > In src/tools: make g_order > It may require that various libraries are already > compiled, which is why > you should build all of gromacs once too (in gmx: > make install). Having > done that once, make g_order should do the trick I > think. > > > > > Please suggest me something, > > regards, > > Priyanka. > > > > > > > > __________________________________________________ > > Do You Yahoo!? > > Tired of spam? Yahoo! Mail has the best spam > protection around > > http://mail.yahoo.com > > _______________________________________________ > > gmx-users mailing list gmx-users at gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the > list. Use the > > www interface or send it to > gmx-users-request at gromacs.org. > > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > -- > Erik Marklund, PhD Student, Molecular Biopcysics > group, > Dept. of Cell and Molecular Biology, Uppsala > University. > Husargatan 3, Box 596, 75124 Uppsala, > Sweden > phone: +46 18 471 4537 fax: +46 18 511 755 > erikm at xray.bmc.uu.se > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the > list. Use the > www interface or send it to > gmx-users-request at gromacs.org. > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From erikm at xray.bmc.uu.se Thu Sep 14 14:18:25 2006 From: erikm at xray.bmc.uu.se (Erik Marklund) Date: Thu, 14 Sep 2006 14:18:25 +0200 Subject: [gmx-users] g_order C code In-Reply-To: <20060914114400.46454.qmail@web39205.mail.mud.yahoo.com> References: <20060914114400.46454.qmail@web39205.mail.mud.yahoo.com> Message-ID: <1158236305.7098.17.camel@jorn.bmc.uu.se> I have never done any lipid order stuff and I don't know that much about the underlying theory, so the only help I can offer concerns progamming only. It seems I have a different version of gmx_order.c, where the problematic parts of the code are around lines 448 and 497. I think, however, that I have found the faulty code. See below. On Thu, 2006-09-14 at 04:44 -0700, priyanka srivastava wrote: > Thank you for your reply. > > I am also curious to know if this is the right way of > doing it. I am not sure of the changes that I have > made in the code. > > Any suggestions on that please? > > Since, when I say "make install" it gives the > following error: > > cc -DHAVE_CONFIG_H -I. -I. -I../../src > -I/usr/X11R6/include -I../../include > -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -O3 > -fomit-frame-pointer -finline-functions -Wall > -Wno-unused -malign-double -funroll-all-loops -MT > gmx_order.lo -MD -MP -MF .deps/gmx_order.Tpo -c > gmx_order.c -o gmx_order.o > gmx_order.c: In function `calc_order': > gmx_order.c:251: called object is not a function > gmx_order.c:252: called object is not a function > gmx_order.c:252: called object is not a function > gmx_order.c: In function `order_plot': > gmx_order.c:300: `i' undeclared (first use in this > function) > gmx_order.c:300: (Each undeclared identifier is > reported only once > gmx_order.c:300: for each function it appears in.) > gmx_order.c:301: called object is not a function > gmx_order.c:302: called object is not a function > gmx_order.c:302: called object is not a function > gmx_order.c:303: called object is not a function > gmx_order.c:304: called object is not a function > make[2]: *** [gmx_order.lo] Error 1 > make[2]: Leaving directory > `/home/histidine/gromacs/gromacs-3.3/src/tools' > make[1]: *** [install-recursive] Error 1 > make[1]: Leaving directory > `/home/histidine/gromacs/gromacs-3.3/src' > make: *** [install-recursive] Error 1 > > > thanks and regards, > Priyanka. > > > > > --- Erik Marklund wrote: > > > On Thu, 2006-09-14 at 02:21 -0700, priyanka > > srivastava wrote: > > > Dear Gromacs users, > > > Hie, > > > > > > I am calculating the order parameters for a > > bilayer > > > patch using g_order analysis tool in gromacs > > version > > > 3.3. > > > > > > I have a total of 48 elements in the patch and I > > want > > > the order parameter value for each and every > > element > > > i.e. a total of say 48 values for order parameter > > > alongwith the average which g_order reports. > > > > > > I tried to fiddle with the code too and tried > > changing > > > the following section as follows: > > > > > > /* average over frames */ > > > for (i = 1; i < nr_tails; i++) { > > > /* svmul(1.0/nr_frames, (*order)[i], > > > (*order)[i]);*/ > > > fprintf(stderr,"Atom %d Tensor: x=%g , y=%g, > > > z=%g\n",i,(*order)(index[i])[XX], > > > (*order)(index[i])[YY], > > > (*order)(index[i])[ZZ]); > > > I think that (*order)(...) makes the compiler try to call the function *order. Since it is in fact not a function, it causes an error. Use square brackets for indexing: (*order)[...]. If I'm right, this causes the error messages for line 251 and 252. > > > > > > and also: > > > > > > sprintf(buf,"Deuterium order parameters"); > > > slOrd = xvgropen(cfile,buf, "Atom", "Scd"); > > > > > > for (i = 1; i < nr_tails; i++) { > > > fprintf(ord,"%12d %12g %12g %12g\n", > > atom, > > > order(index[i])[XX], > > > order(index[i])[YY], > > > order(index[i])[ZZ]); > > > fprintf(slOrd,"%12d %12g\n", atom, -1 * > > > (0.6667 * order(index[i])[XX] + > > > > > 0.333 > > > * order(index[i])[YY])); > > > Indeed, i is undefined in order_plot. And once again you use parentheses for indexing. This causes the remaining errors. > > > The problem is I am not sure if that is the right > > way > > > of doing this. Please suggest me something. Also > > once > > > these changes have been incorporated in the C > > program > > > how do I generate the exe of g_order. Gcc gives > > many > > > undefined errors. > > > > In src/tools: make g_order > > It may require that various libraries are already > > compiled, which is why > > you should build all of gromacs once too (in gmx: > > make install). Having > > done that once, make g_order should do the trick I > > think. > > > > > > > > Please suggest me something, > > > regards, > > > Priyanka. > > > > > > > > > > > > __________________________________________________ > > > Do You Yahoo!? > > > Tired of spam? Yahoo! Mail has the best spam > > protection around > > > http://mail.yahoo.com > > > _______________________________________________ > > > gmx-users mailing list gmx-users at gromacs.org > > > http://www.gromacs.org/mailman/listinfo/gmx-users > > > Please don't post (un)subscribe requests to the > > list. Use the > > > www interface or send it to > > gmx-users-request at gromacs.org. > > > Can't post? Read > > http://www.gromacs.org/mailing_lists/users.php > > -- > > Erik Marklund, PhD Student, Molecular Biopcysics > > group, > > Dept. of Cell and Molecular Biology, Uppsala > > University. > > Husargatan 3, Box 596, 75124 Uppsala, > > Sweden > > phone: +46 18 471 4537 fax: +46 18 511 755 > > erikm at xray.bmc.uu.se > > > > _______________________________________________ > > gmx-users mailing list gmx-users at gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the > > list. Use the > > www interface or send it to > > gmx-users-request at gromacs.org. > > Can't post? Read > > http://www.gromacs.org/mailing_lists/users.php > > > > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Erik Marklund, PhD Student, Molecular Biopcysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 erikm at xray.bmc.uu.se From priyankaps4 at yahoo.com Thu Sep 14 14:48:27 2006 From: priyankaps4 at yahoo.com (priyanka srivastava) Date: Thu, 14 Sep 2006 05:48:27 -0700 (PDT) Subject: [gmx-users] g_order C code In-Reply-To: <1158236305.7098.17.camel@jorn.bmc.uu.se> Message-ID: <20060914124827.30991.qmail@web39213.mail.mud.yahoo.com> thanks again for your prompt reply. Okey, and I am not good at programming at all :-) By looking at the gmx_order.c program could u tell me which flag is i.e. index[i] or only [i] is indicating the elements of a group? Supppose there are 14 groups (i guess denoted by ngrps in the code) and each group in turn contains 48 elements, so what I am interested to know is the flag that is associated with the second part i.e. individual elements. regards, Pri... --- Erik Marklund wrote: > I have never done any lipid order stuff and I don't > know that much about > the underlying theory, so the only help I can offer > concerns progamming > only. > > It seems I have a different version of gmx_order.c, > where the > problematic parts of the code are around lines 448 > and 497. I think, > however, that I have found the faulty code. See > below. > > On Thu, 2006-09-14 at 04:44 -0700, priyanka > srivastava wrote: > > Thank you for your reply. > > > > I am also curious to know if this is the right way > of > > doing it. I am not sure of the changes that I have > > made in the code. > > > > Any suggestions on that please? > > > > Since, when I say "make install" it gives the > > following error: > > > > cc -DHAVE_CONFIG_H -I. -I. -I../../src > > -I/usr/X11R6/include -I../../include > > -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -O3 > > -fomit-frame-pointer -finline-functions -Wall > > -Wno-unused -malign-double -funroll-all-loops -MT > > gmx_order.lo -MD -MP -MF .deps/gmx_order.Tpo -c > > gmx_order.c -o gmx_order.o > > gmx_order.c: In function `calc_order': > > gmx_order.c:251: called object is not a function > > gmx_order.c:252: called object is not a function > > gmx_order.c:252: called object is not a function > > gmx_order.c: In function `order_plot': > > gmx_order.c:300: `i' undeclared (first use in this > > function) > > gmx_order.c:300: (Each undeclared identifier is > > reported only once > > gmx_order.c:300: for each function it appears in.) > > gmx_order.c:301: called object is not a function > > gmx_order.c:302: called object is not a function > > gmx_order.c:302: called object is not a function > > gmx_order.c:303: called object is not a function > > gmx_order.c:304: called object is not a function > > make[2]: *** [gmx_order.lo] Error 1 > > make[2]: Leaving directory > > `/home/histidine/gromacs/gromacs-3.3/src/tools' > > make[1]: *** [install-recursive] Error 1 > > make[1]: Leaving directory > > `/home/histidine/gromacs/gromacs-3.3/src' > > make: *** [install-recursive] Error 1 > > > > > > thanks and regards, > > Priyanka. > > > > > > > > > > --- Erik Marklund wrote: > > > > > On Thu, 2006-09-14 at 02:21 -0700, priyanka > > > srivastava wrote: > > > > Dear Gromacs users, > > > > Hie, > > > > > > > > I am calculating the order parameters for a > > > bilayer > > > > patch using g_order analysis tool in gromacs > > > version > > > > 3.3. > > > > > > > > I have a total of 48 elements in the patch and > I > > > want > > > > the order parameter value for each and every > > > element > > > > i.e. a total of say 48 values for order > parameter > > > > alongwith the average which g_order reports. > > > > > > > > I tried to fiddle with the code too and tried > > > changing > > > > the following section as follows: > > > > > > > > /* average over frames */ > > > > for (i = 1; i < nr_tails; i++) { > > > > /* svmul(1.0/nr_frames, (*order)[i], > > > > (*order)[i]);*/ > > > > fprintf(stderr,"Atom %d Tensor: x=%g , > y=%g, > > > > z=%g\n",i,(*order)(index[i])[XX], > > > > (*order)(index[i])[YY], > > > > (*order)(index[i])[ZZ]); > > > > > > I think that (*order)(...) makes the compiler try to > call the function > *order. Since it is in fact not a function, it > causes an error. Use > square brackets for indexing: (*order)[...]. If I'm > right, this causes > the error messages for line 251 and 252. > > > > > > > > > and also: > > > > > > > > sprintf(buf,"Deuterium order parameters"); > > > > slOrd = xvgropen(cfile,buf, "Atom", > "Scd"); > > > > > > > > for (i = 1; i < nr_tails; i++) { > > > > fprintf(ord,"%12d %12g %12g > %12g\n", > > > atom, > > > > order(index[i])[XX], > > > > order(index[i])[YY], > > > > order(index[i])[ZZ]); > > > > fprintf(slOrd,"%12d %12g\n", atom, -1 > * > > > > (0.6667 * order(index[i])[XX] + > > > > > > > > 0.333 > > > > * order(index[i])[YY])); > > > > > > Indeed, i is undefined in order_plot. And once again > you use parentheses > for indexing. This causes the remaining errors. > > > > > The problem is I am not sure if that is the > right > > > way > > > > of doing this. Please suggest me something. > Also > > > once > > > > these changes have been incorporated in the C > > > program > > > > how do I generate the exe of g_order. Gcc > gives > > > many > > > > undefined errors. > > > > > > In src/tools: make g_order > > > It may require that various libraries are > already > > > compiled, which is why > > > you should build all of gromacs once too (in > gmx: > > > make install). Having > > > done that once, make g_order should do the trick > I > > > think. > > > > > > > > > > > Please suggest me something, > > > > regards, > > > > Priyanka. > > > > > > > > > > > > > > > > > __________________________________________________ > > > > Do You Yahoo!? > > > > Tired of spam? Yahoo! Mail has the best spam > > > protection around > > > > http://mail.yahoo.com > > > > > _______________________________________________ > > > > gmx-users mailing list > gmx-users at gromacs.org > > > > > http://www.gromacs.org/mailman/listinfo/gmx-users > > > > Please don't post (un)subscribe requests to > the > > > list. Use the > > > > www interface or send it to > > > gmx-users-request at gromacs.org. > > > > Can't post? Read > > > http://www.gromacs.org/mailing_lists/users.php > > > -- > > > Erik Marklund, PhD Student, Molecular Biopcysics > > > group, > > > Dept. of Cell and Molecular Biology, Uppsala > > > University. > > > Husargatan 3, Box 596, 75124 Uppsala, > > > Sweden > > > phone: +46 18 471 4537 fax: +46 18 511 > 755 > > > erikm at xray.bmc.uu.se > > > > > > _______________________________________________ > > > gmx-users mailing list gmx-users at gromacs.org > > > > http://www.gromacs.org/mailman/listinfo/gmx-users > === message truncated === __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From navratna.vajpai at unibas.ch Thu Sep 14 15:00:13 2006 From: navratna.vajpai at unibas.ch (Navratna Vajpai) Date: Thu, 14 Sep 2006 15:00:13 +0200 Subject: Fwd: [gmx-users] Hi... References: <202973AA-D3F2-40A0-A83A-53DA379505D2@unibas.ch> Message-ID: <71040B4B-C03C-4A71-88D0-3DB34FF08A7E@unibas.ch> Hi all.. I wrote this mail yesterday. But could not receive any reply till now. So if someone can suggest something about it. That would be nice. Best regards Nav Begin forwarded message: > From: Navratna Vajpai > Date: September 13, 2006 10:32:21 AM GMT+02:00 > To: Discussion list for GROMACS users > Subject: [gmx-users] Hi... > Reply-To: Discussion list for GROMACS users > > Dear All > Hi.. > This is in regard to your previously replied mail regarding the use > of GROMOS96 or OPLS-AA or AMBER force field. > As you said it depends upon the users taste which one to use. This > means that the three on a broad manner should give convergence of > the analyzed data set. > Infact from my simulation runs using oplss-aa and gromos96, I > didn't found that. I tried using the GROMOS96 and opls-aa force > field on my small peptides for a period of 20ns and found that with > opls-aa even the phi-psi combination of the individual amino acids > were incorrect. Actually this always puzzled me to make a choice > for the Force field. The rest of the script was unchanged for the > two runs. > Could you please comment on the above results? Is there any way > really to judge which force field is to be chosen for particular > type of analysis? > Best regards > Nav > > ******************************************* > Navratna Vajpai > Ph. D student in Prof. Grzesiek's laboratory > Department of Structural Biology > Biozentrum, University of Basel > Klingelbergstrasse 70, > CH-4056 > Basel, Switzerland. > Phone- +41 61 267 2080(O) > +41 78 744 0810(M) > > navratna.vajpai at unibas.ch > > > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php ******************************************* Navratna Vajpai Ph. D student in Prof. Grzesiek's laboratory Department of Structural Biology Biozentrum, University of Basel Klingelbergstrasse 70, CH-4056 Basel, Switzerland. Phone- +41 61 267 2080(O) +41 78 744 0810(M) navratna.vajpai at unibas.ch -------------- next part -------------- An HTML attachment was scrubbed... URL: From spoel at xray.bmc.uu.se Thu Sep 14 15:36:47 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Thu, 14 Sep 2006 06:36:47 -0700 Subject: Fwd: [gmx-users] Hi... In-Reply-To: <71040B4B-C03C-4A71-88D0-3DB34FF08A7E@unibas.ch> References: <202973AA-D3F2-40A0-A83A-53DA379505D2@unibas.ch> <71040B4B-C03C-4A71-88D0-3DB34FF08A7E@unibas.ch> Message-ID: <45095AEF.3070100@xray.bmc.uu.se> Navratna Vajpai wrote: > Hi all.. > I wrote this mail yesterday. But could not receive any reply till now. > So if someone can suggest something about it. That would be nice. > Best regards > Nav > > Begin forwarded message: > >> *From: *Navratna Vajpai > > >> *Date: *September 13, 2006 10:32:21 AM GMT+02:00 >> *To: *Discussion list for GROMACS users > > >> *Subject: **[gmx-users] Hi...* >> *Reply-To: *Discussion list for GROMACS users > > >> >> Dear All >> Hi.. >> This is in regard to your previously replied mail regarding the use of >> GROMOS96 or OPLS-AA or AMBER force field. >> As you said it depends upon the users taste which one to use. This >> means that the three on a broad manner should give convergence of >> the analyzed data set. >> Infact from my simulation runs using oplss-aa and gromos96, I didn't >> found that. I tried using the GROMOS96 and opls-aa force field on my >> small peptides for a period of 20ns and found that with opls-aa even >> the phi-psi combination of the individual amino acids were incorrect. >> Actually this always puzzled me to make a choice for the Force field. >> The rest of the script was unchanged for the two runs. >> Could you please comment on the above results? Is there any way really >> to judge which force field is to be chosen for particular type of >> analysis? >> Best regards >> Nav >> what do you mean with incorrect? your question is quite vague. the g_rama program works only for GROMOS like force fields unfortunately but that doesn't mean the phi/psi are wrong. What would be the "correct" result anyway? Maybe your peptide unfolds. -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From erikm at xray.bmc.uu.se Thu Sep 14 15:32:31 2006 From: erikm at xray.bmc.uu.se (Erik Marklund) Date: Thu, 14 Sep 2006 15:32:31 +0200 Subject: [gmx-users] g_order C code In-Reply-To: <20060914124827.30991.qmail@web39213.mail.mud.yahoo.com> References: <20060914124827.30991.qmail@web39213.mail.mud.yahoo.com> Message-ID: <1158240751.7098.53.camel@jorn.bmc.uu.se> Hi again. I've taken a quick glace at the code, trying to figure out what the different structures and variables are all about. Here goes... order seem to be an array of pointers to 3D-vectors (type rvec, that is). ngrps is in this case actually the number of atoms in a group. Therefore (*order)[i][XX] refers to the x-component of the order-vector belonging to atom i. Have a look at gmx/include/types/block.h. There toy will find some descriptions of variables nrgrps ( = nr in block.h), index and more. That's my interpretation of things. Still I know little about the order parameter, so I don't know if the above makes sense or not. Hope that helps. /Erik On Thu, 2006-09-14 at 05:48 -0700, priyanka srivastava wrote: > thanks again for your prompt reply. > > Okey, and I am not good at programming at all :-) > > By looking at the gmx_order.c program could u tell me > which flag is i.e. index[i] or only [i] is indicating > the elements of a group? > > Supppose there are 14 groups (i guess denoted by ngrps > in the code) and each group in turn contains 48 > elements, so what I am interested to know is the flag > that is associated with the second part i.e. > individual elements. > > regards, > Pri... > > --- Erik Marklund wrote: > > > I have never done any lipid order stuff and I don't > > know that much about > > the underlying theory, so the only help I can offer > > concerns progamming > > only. > > > > It seems I have a different version of gmx_order.c, > > where the > > problematic parts of the code are around lines 448 > > and 497. I think, > > however, that I have found the faulty code. See > > below. > > > > On Thu, 2006-09-14 at 04:44 -0700, priyanka > > srivastava wrote: > > > Thank you for your reply. > > > > > > I am also curious to know if this is the right way > > of > > > doing it. I am not sure of the changes that I have > > > made in the code. > > > > > > Any suggestions on that please? > > > > > > Since, when I say "make install" it gives the > > > following error: > > > > > > cc -DHAVE_CONFIG_H -I. -I. -I../../src > > > -I/usr/X11R6/include -I../../include > > > -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -O3 > > > -fomit-frame-pointer -finline-functions -Wall > > > -Wno-unused -malign-double -funroll-all-loops -MT > > > gmx_order.lo -MD -MP -MF .deps/gmx_order.Tpo -c > > > gmx_order.c -o gmx_order.o > > > gmx_order.c: In function `calc_order': > > > gmx_order.c:251: called object is not a function > > > gmx_order.c:252: called object is not a function > > > gmx_order.c:252: called object is not a function > > > gmx_order.c: In function `order_plot': > > > gmx_order.c:300: `i' undeclared (first use in this > > > function) > > > gmx_order.c:300: (Each undeclared identifier is > > > reported only once > > > gmx_order.c:300: for each function it appears in.) > > > gmx_order.c:301: called object is not a function > > > gmx_order.c:302: called object is not a function > > > gmx_order.c:302: called object is not a function > > > gmx_order.c:303: called object is not a function > > > gmx_order.c:304: called object is not a function > > > make[2]: *** [gmx_order.lo] Error 1 > > > make[2]: Leaving directory > > > `/home/histidine/gromacs/gromacs-3.3/src/tools' > > > make[1]: *** [install-recursive] Error 1 > > > make[1]: Leaving directory > > > `/home/histidine/gromacs/gromacs-3.3/src' > > > make: *** [install-recursive] Error 1 > > > > > > > > > thanks and regards, > > > Priyanka. > > > > > > > > > > > > > > > --- Erik Marklund wrote: > > > > > > > On Thu, 2006-09-14 at 02:21 -0700, priyanka > > > > srivastava wrote: > > > > > Dear Gromacs users, > > > > > Hie, > > > > > > > > > > I am calculating the order parameters for a > > > > bilayer > > > > > patch using g_order analysis tool in gromacs > > > > version > > > > > 3.3. > > > > > > > > > > I have a total of 48 elements in the patch and > > I > > > > want > > > > > the order parameter value for each and every > > > > element > > > > > i.e. a total of say 48 values for order > > parameter > > > > > alongwith the average which g_order reports. > > > > > > > > > > I tried to fiddle with the code too and tried > > > > changing > > > > > the following section as follows: > > > > > > > > > > /* average over frames */ > > > > > for (i = 1; i < nr_tails; i++) { > > > > > /* svmul(1.0/nr_frames, (*order)[i], > > > > > (*order)[i]);*/ > > > > > fprintf(stderr,"Atom %d Tensor: x=%g , > > y=%g, > > > > > z=%g\n",i,(*order)(index[i])[XX], > > > > > (*order)(index[i])[YY], > > > > > (*order)(index[i])[ZZ]); > > > > > > > > > I think that (*order)(...) makes the compiler try to > > call the function > > *order. Since it is in fact not a function, it > > causes an error. Use > > square brackets for indexing: (*order)[...]. If I'm > > right, this causes > > the error messages for line 251 and 252. > > > > > > > > > > > > and also: > > > > > > > > > > sprintf(buf,"Deuterium order parameters"); > > > > > slOrd = xvgropen(cfile,buf, "Atom", > > "Scd"); > > > > > > > > > > for (i = 1; i < nr_tails; i++) { > > > > > fprintf(ord,"%12d %12g %12g > > %12g\n", > > > > atom, > > > > > order(index[i])[XX], > > > > > order(index[i])[YY], > > > > > order(index[i])[ZZ]); > > > > > fprintf(slOrd,"%12d %12g\n", atom, -1 > > * > > > > > (0.6667 * order(index[i])[XX] + > > > > > > > > > > > 0.333 > > > > > * order(index[i])[YY])); > > > > > > > > > Indeed, i is undefined in order_plot. And once again > > you use parentheses > > for indexing. This causes the remaining errors. > > > > > > > The problem is I am not sure if that is the > > right > > > > way > > > > > of doing this. Please suggest me something. > > Also > > > > once > > > > > these changes have been incorporated in the C > > > > program > > > > > how do I generate the exe of g_order. Gcc > > gives > > > > many > > > > > undefined errors. > > > > > > > > In src/tools: make g_order > > > > It may require that various libraries are > > already > > > > compiled, which is why > > > > you should build all of gromacs once too (in > > gmx: > > > > make install). Having > > > > done that once, make g_order should do the trick > > I > > > > think. > > > > > > > > > > > > > > Please suggest me something, > > > > > regards, > > > > > Priyanka. > > > > > > > > > > > > > > > > > > > > > > __________________________________________________ > > > > > Do You Yahoo!? > > > > > Tired of spam? Yahoo! Mail has the best spam > > > > protection around > > > > > http://mail.yahoo.com > > > > > > > _______________________________________________ > > > > > gmx-users mailing list > > gmx-users at gromacs.org > > > > > > > http://www.gromacs.org/mailman/listinfo/gmx-users > > > > > Please don't post (un)subscribe requests to > > the > > > > list. Use the > > > > > www interface or send it to > > > > gmx-users-request at gromacs.org. > > > > > Can't post? Read > > > > http://www.gromacs.org/mailing_lists/users.php > > > > -- > > > > Erik Marklund, PhD Student, Molecular Biopcysics > > > > group, > > > > Dept. of Cell and Molecular Biology, Uppsala > > > > University. > > > > Husargatan 3, Box 596, 75124 Uppsala, > > > > Sweden > > > > phone: +46 18 471 4537 fax: +46 18 511 > > 755 > > > > erikm at xray.bmc.uu.se > > > > > > > > _______________________________________________ > > > > gmx-users mailing list gmx-users at gromacs.org > > > > > > http://www.gromacs.org/mailman/listinfo/gmx-users > > > === message truncated === > > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Erik Marklund, PhD Student, Molecular Biopcysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 erikm at xray.bmc.uu.se From navratna.vajpai at unibas.ch Thu Sep 14 15:50:05 2006 From: navratna.vajpai at unibas.ch (Navratna Vajpai) Date: Thu, 14 Sep 2006 15:50:05 +0200 Subject: [gmx-users] Hi... In-Reply-To: <45095AEF.3070100@xray.bmc.uu.se> References: <202973AA-D3F2-40A0-A83A-53DA379505D2@unibas.ch> <71040B4B-C03C-4A71-88D0-3DB34FF08A7E@unibas.ch> <45095AEF.3070100@xray.bmc.uu.se> Message-ID: <445B8F54-B28E-4C16-A81C-4D89A83D9854@unibas.ch> Sorry for not so explicitly explaining the things.. Here it goes I have a nona peptide and I ran a MD of 20ns using OPLS-AA force field. when I used the OPLS-AA the phi angles came out to be -ve for three of the amino acids. which is stericaly not allowed. But when I ran it using GROMOS I found all the phi-psi combinations with a negative phi value distribution. But now I am lost as you have said it works only for GROMOS like force field. Why? and if that so I have got -ve phi distribution for the other phi-psi plots. My other question remained unanswered even now. Is there any way really to judge which force field is to be chosen for particular type of analysis? Best regards Thanks On Sep 14, 2006, at 3:36 PM, David van der Spoel wrote: > Navratna Vajpai wrote: >> Hi all.. I wrote this mail yesterday. But could not receive any >> reply till now. So if someone can suggest something about it. That >> would be nice. Best regards >> Nav >> Begin forwarded message: >>> *From: *Navratna Vajpai >> > >>> *Date: *September 13, 2006 10:32:21 AM GMT+02:00 >>> *To: *Discussion list for GROMACS users >> > >>> *Subject: **[gmx-users] Hi...* >>> *Reply-To: *Discussion list for GROMACS users >> users at gromacs.org > >>> >>> Dear All >>> Hi.. This is in regard to your previously replied mail regarding >>> the use of GROMOS96 or OPLS-AA or AMBER force field. >>> As you said it depends upon the users taste which one to use. >>> This means that the three on a broad manner should give >>> convergence of the analyzed data set. Infact from my simulation >>> runs using oplss-aa and gromos96, I didn't found that. I tried >>> using the GROMOS96 and opls-aa force field on my small peptides >>> for a period of 20ns and found that with opls-aa even the phi-psi >>> combination of the individual amino acids were incorrect. >>> Actually this always puzzled me to make a choice for the Force >>> field. The rest of the script was unchanged for the two runs. >>> Could you please comment on the above results? Is there any way >>> really to judge which force field is to be chosen for particular >>> type of analysis? >>> Best regards >>> Nav >>> > > > what do you mean with incorrect? your question is quite vague. > > the g_rama program works only for GROMOS like force fields > unfortunately but that doesn't mean the phi/psi are wrong. What > would be the "correct" result anyway? Maybe your peptide unfolds. > > -- > David. > ______________________________________________________________________ > __ > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > ++++ > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php ******************************************* Navratna Vajpai Ph. D student in Prof. Grzesiek's laboratory Department of Structural Biology Biozentrum, University of Basel Klingelbergstrasse 70, CH-4056 Basel, Switzerland. Phone- +41 61 267 2080(O) +41 78 744 0810(M) navratna.vajpai at unibas.ch -------------- next part -------------- An HTML attachment was scrubbed... URL: From YGMu at ntu.edu.sg Thu Sep 14 16:02:10 2006 From: YGMu at ntu.edu.sg (Mu Yuguang (Dr)) Date: Thu, 14 Sep 2006 22:02:10 +0800 Subject: [gmx-users] Hi... Message-ID: <48BABA4E8A54DF4AAF9CCF36D614027302E1B763@EXCHANGE23.staff.main.ntu.edu.sg> OPLS-aa force field is good for beta structure, it is not so good for alpha helix study. Amber99f force field is good for alpha helix , but not good for beta structure Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php ________________________________ From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Navratna Vajpai Sent: Thursday, September 14, 2006 9:50 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Hi... Sorry for not so explicitly explaining the things.. Here it goes I have a nona peptide and I ran a MD of 20ns using OPLS-AA force field. when I used the OPLS-AA the phi angles came out to be -ve for three of the amino acids. which is stericaly not allowed. But when I ran it using GROMOS I found all the phi-psi combinations with a negative phi value distribution. But now I am lost as you have said it works only for GROMOS like force field. Why? and if that so I have got -ve phi distribution for the other phi-psi plots. My other question remained unanswered even now. Is there any way really to judge which force field is to be chosen for particular type of analysis? Best regards Thanks On Sep 14, 2006, at 3:36 PM, David van der Spoel wrote: Navratna Vajpai wrote: Hi all.. I wrote this mail yesterday. But could not receive any reply till now. So if someone can suggest something about it. That would be nice. Best regards Nav Begin forwarded message: *From: *Navratna Vajpai > *Date: *September 13, 2006 10:32:21 AM GMT+02:00 *To: *Discussion list for GROMACS users > *Subject: **[gmx-users] Hi...* *Reply-To: *Discussion list for GROMACS users > Dear All Hi.. This is in regard to your previously replied mail regarding the use of GROMOS96 or OPLS-AA or AMBER force field. As you said it depends upon the users taste which one to use. This means that the three on a broad manner should give convergence of the analyzed data set. Infact from my simulation runs using oplss-aa and gromos96, I didn't found that. I tried using the GROMOS96 and opls-aa force field on my small peptides for a period of 20ns and found that with opls-aa even the phi-psi combination of the individual amino acids were incorrect. Actually this always puzzled me to make a choice for the Force field. The rest of the script was unchanged for the two runs. Could you please comment on the above results? Is there any way really to judge which force field is to be chosen for particular type of analysis? Best regards Nav what do you mean with incorrect? your question is quite vague. the g_rama program works only for GROMOS like force fields unfortunately but that doesn't mean the phi/psi are wrong. What would be the "correct" result anyway? Maybe your peptide unfolds. -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ******************************************* Navratna Vajpai Ph. D student in Prof. Grzesiek's laboratory Department of Structural Biology Biozentrum, University of Basel Klingelbergstrasse 70, CH-4056 Basel, Switzerland. Phone- +41 61 267 2080(O) +41 78 744 0810(M) navratna.vajpai at unibas.ch -------------- next part -------------- An HTML attachment was scrubbed... URL: From fefan at utmb.edu Thu Sep 14 16:08:33 2006 From: fefan at utmb.edu (Fan, Fenghui ) Date: Thu, 14 Sep 2006 09:08:33 -0500 Subject: [gmx-users] why the backbone can be broken during MD process Message-ID: Dear all, Will you please tell me why the backbone can be broken during MD process and how can we fix them? I am looking forward to getting your reply. Best regards. Fenghui Fan From asillanp at csc.fi Thu Sep 14 16:11:00 2006 From: asillanp at csc.fi (=?ISO-8859-1?Q?Atte_Sillanp=E4=E4?=) Date: Thu, 14 Sep 2006 17:11:00 +0300 (EEST) Subject: [gmx-users] short range nonbondeds = 0 in power4 Message-ID: Hi, I've run into a mysterious problem. The versions 3.3. and 3.3.1 compile and execute, but the short range coulomb and LJ energies come out as zero when using the mpi-version. Serial code works ok (mpi version gives zero if run using just one cpu). No errors, no warnings. I've tried using both fftw 2.1.5 and 3.0.1, tried dropping the optimization level to -O1, -qstrict, --disable-ppc-altivec, ... The config options were (e.g.) as follows: setenv CPPFLAGS -I/v/aix52_rs/appl/math/fftw/fftw-3.0.1_32/include setenv LDFLAGS -L/v/aix52_rs/appl/math/fftw/fftw-3.0.1_32/lib setenv MPICC mpcc_r ./configure --prefix=/wrk/gmx --program-suffix="_mpi" --enable-mpi --disable-nice --enable-threads -with-fft=fftw3 >From the beginning of the config.log: hostname = p690m uname -m = 00105CDA4C00 uname -r = 2 uname -s = AIX uname -v = 5 /usr/bin/uname -p = powerpc /bin/uname -X = unknown /bin/arch = unknown /usr/bin/arch -k = unknown /usr/convex/getsysinfo = unknown hostinfo = unknown /bin/machine = unknown /usr/bin/oslevel = 5.2.0.0 /bin/universe = unknown We don't get the kind of errors described earlier for power4 on the list. I actually managed to make a working mdrun_mpi from 3.3 last year using the same options, but after poe/ppe/... update on the power4 machine I get this odd behaviour also on the 3.3 version. Any ideas? What to tweak, where to look? Cheers, Atte From spoel at xray.bmc.uu.se Thu Sep 14 16:16:33 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Thu, 14 Sep 2006 07:16:33 -0700 Subject: [gmx-users] why the backbone can be broken during MD process In-Reply-To: References: Message-ID: <45096441.5020201@xray.bmc.uu.se> Fan, Fenghui wrote: > Dear all, > > Will you please tell me why the backbone can be broken during MD process and how can we fix them? > > I am looking forward to getting your reply. it can not. please be more specific. > > Best regards. > > Fenghui Fan > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From spoel at xray.bmc.uu.se Thu Sep 14 16:17:41 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Thu, 14 Sep 2006 07:17:41 -0700 Subject: [gmx-users] short range nonbondeds = 0 in power4 In-Reply-To: References: Message-ID: <45096485.3080603@xray.bmc.uu.se> Atte Sillanp?? wrote: > Hi, > > I've run into a mysterious problem. The versions 3.3. and 3.3.1 compile > and execute, but the short range coulomb and LJ energies come out as > zero when using the mpi-version. Serial code works ok (mpi version gives > zero if run using just one cpu). No errors, no warnings. > > I've tried using both fftw 2.1.5 and 3.0.1, tried dropping the > optimization level to -O1, -qstrict, --disable-ppc-altivec, ... > > The config options were (e.g.) as follows: > > setenv CPPFLAGS -I/v/aix52_rs/appl/math/fftw/fftw-3.0.1_32/include > setenv LDFLAGS -L/v/aix52_rs/appl/math/fftw/fftw-3.0.1_32/lib > setenv MPICC mpcc_r > ./configure --prefix=/wrk/gmx --program-suffix="_mpi" --enable-mpi > --disable-nice --enable-threads -with-fft=fftw3 > >> From the beginning of the config.log: > > hostname = p690m > uname -m = 00105CDA4C00 > uname -r = 2 > uname -s = AIX > uname -v = 5 > > /usr/bin/uname -p = powerpc > /bin/uname -X = unknown > > /bin/arch = unknown > /usr/bin/arch -k = unknown > /usr/convex/getsysinfo = unknown > hostinfo = unknown > /bin/machine = unknown > /usr/bin/oslevel = 5.2.0.0 > /bin/universe = unknown > > We don't get the kind of errors described earlier for power4 on the > list. I actually managed to make a working mdrun_mpi from 3.3 last year > using the same options, but after poe/ppe/... update on the power4 > machine I get this odd behaviour also on the 3.3 version. Any ideas? > What to tweak, where to look? > > Cheers, > > Atte > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php if you suspect PME, then try running without it. -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From spoel at xray.bmc.uu.se Thu Sep 14 16:18:26 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Thu, 14 Sep 2006 07:18:26 -0700 Subject: [gmx-users] Hi... In-Reply-To: <48BABA4E8A54DF4AAF9CCF36D614027302E1B763@EXCHANGE23.staff.main.ntu.edu.sg> References: <48BABA4E8A54DF4AAF9CCF36D614027302E1B763@EXCHANGE23.staff.main.ntu.edu.sg> Message-ID: <450964B2.5050005@xray.bmc.uu.se> Mu Yuguang (Dr) wrote: > OPLS-aa force field is good for beta structure, it is not so good for > alpha helix study. > > Amber99f force field is good for alpha helix , but not good for beta > structure > Very encouraging... -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From spoel at xray.bmc.uu.se Thu Sep 14 16:22:14 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Thu, 14 Sep 2006 07:22:14 -0700 Subject: [gmx-users] Hi... In-Reply-To: <445B8F54-B28E-4C16-A81C-4D89A83D9854@unibas.ch> References: <202973AA-D3F2-40A0-A83A-53DA379505D2@unibas.ch> <71040B4B-C03C-4A71-88D0-3DB34FF08A7E@unibas.ch> <45095AEF.3070100@xray.bmc.uu.se> <445B8F54-B28E-4C16-A81C-4D89A83D9854@unibas.ch> Message-ID: <45096596.2010302@xray.bmc.uu.se> Navratna Vajpai wrote: > Sorry for not so explicitly explaining the things.. Here it goes > I have a nona peptide and I ran a MD of 20ns using OPLS-AA force field. > when I used the OPLS-AA the phi angles came out to be -ve for three of > the amino acids. which is stericaly not allowed. But when I ran it using > GROMOS I found all the phi-psi combinations with a negative phi value > distribution. But now I am lost as you have said it works only for > GROMOS like force field. Why? problem in the anaysis program (assuming you used g_rama). please use g_angle. > and if that so I have got -ve phi distribution for the other phi-psi plots. > My other question remained unanswered even now. Is there any way really > to judge which force field is to be chosen for particular type of analysis? > Best regards > Thanks > what do you mean with -ve ? force field can be evaluated in many ways. Start by checking this paper and references in them: Hydration thermodynamic properties of amino Acid analogues: a systematic comparison of biomolecular force fields and water models. * Hess B, * van der Vegt NF. J Phys Chem B Condens Matter Mater Surf Interfaces Biophys. 2006 Sep 7;110(35):17616-26. -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From navratna.vajpai at unibas.ch Thu Sep 14 16:22:01 2006 From: navratna.vajpai at unibas.ch (Navratna Vajpai) Date: Thu, 14 Sep 2006 16:22:01 +0200 Subject: [gmx-users] Hi... In-Reply-To: <45096596.2010302@xray.bmc.uu.se> References: <202973AA-D3F2-40A0-A83A-53DA379505D2@unibas.ch> <71040B4B-C03C-4A71-88D0-3DB34FF08A7E@unibas.ch> <45095AEF.3070100@xray.bmc.uu.se> <445B8F54-B28E-4C16-A81C-4D89A83D9854@unibas.ch> <45096596.2010302@xray.bmc.uu.se> Message-ID: <2AF2E2AD-2866-42AA-978D-7A7AF499C021@unibas.ch> You are right .. I have used g_rama for the phi-psi values. I will try g_angle as well. With -ve i meant negative values for the phi angle. As far as I understand negative phi values are sterically not allowed. let me check with the g_angle as well. Thanks for the answer as well the reference. best regards Nav On Sep 14, 2006, at 4:22 PM, David van der Spoel wrote: > Navratna Vajpai wrote: >> Sorry for not so explicitly explaining the things.. Here it goes >> I have a nona peptide and I ran a MD of 20ns using OPLS-AA force >> field. when I used the OPLS-AA the phi angles came out to be -ve >> for three of the amino acids. which is stericaly not allowed. But >> when I ran it using GROMOS I found all the phi-psi combinations >> with a negative phi value distribution. But now I am lost as you >> have said it works only for GROMOS like force field. Why? > > problem in the anaysis program (assuming you used g_rama). please > use g_angle. > >> and if that so I have got -ve phi distribution for the other phi- >> psi plots. My other question remained unanswered even now. Is >> there any way really to judge which force field is to be chosen >> for particular type of analysis? >> Best regards Thanks >> > > what do you mean with -ve ? > > force field can be evaluated in many ways. > > Start by checking this paper and references in them: > > Hydration thermodynamic properties of amino Acid analogues: a > systematic comparison of biomolecular force fields and water models. > > * Hess B, > * van der Vegt NF. > > J Phys Chem B Condens Matter Mater Surf Interfaces Biophys. 2006 > Sep 7;110(35):17616-26. > > -- > David. > ______________________________________________________________________ > __ > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > ++++ > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php ******************************************* Navratna Vajpai Ph. D student in Prof. Grzesiek's laboratory Department of Structural Biology Biozentrum, University of Basel Klingelbergstrasse 70, CH-4056 Basel, Switzerland. Phone- +41 61 267 2080(O) +41 78 744 0810(M) navratna.vajpai at unibas.ch -------------- next part -------------- An HTML attachment was scrubbed... URL: From Mark.Abraham at anu.edu.au Thu Sep 14 16:32:16 2006 From: Mark.Abraham at anu.edu.au (Mark Abraham) Date: Fri, 15 Sep 2006 00:32:16 +1000 Subject: [gmx-users] why the backbone can be broken during MD process In-Reply-To: References: Message-ID: <450967F0.6080103@anu.edu.au> Fan, Fenghui wrote: > Dear all, > > Will you please tell me why the backbone can be broken during MD process and how can we fix them? It can only be broken if you haven't defined it to be whole, or have done something mind-numbingly hideous elsewhere :-) Check your .top file Mark From dong at pampas.chem.purdue.edu Thu Sep 14 16:46:52 2006 From: dong at pampas.chem.purdue.edu (Dongsheng Zhang) Date: Thu, 14 Sep 2006 10:46:52 -0400 Subject: Fwd: [gmx-users] Hi... In-Reply-To: <45095AEF.3070100@xray.bmc.uu.se> References: <202973AA-D3F2-40A0-A83A-53DA379505D2@unibas.ch> <71040B4B-C03C-4A71-88D0-3DB34FF08A7E@unibas.ch> <45095AEF.3070100@xray.bmc.uu.se> Message-ID: <1158245212.19729.8.camel@pampas.chem.purdue.edu> On Thu, 2006-09-14 at 06:36 -0700, David van der Spoel wrote: > Navratna Vajpai wrote: > > Hi all.. > > I wrote this mail yesterday. But could not receive any reply till now. > > So if someone can suggest something about it. That would be nice. > > Best regards > > Nav > > > > Begin forwarded message: > > > >> *From: *Navratna Vajpai >> > > >> *Date: *September 13, 2006 10:32:21 AM GMT+02:00 > >> *To: *Discussion list for GROMACS users >> > > >> *Subject: **[gmx-users] Hi...* > >> *Reply-To: *Discussion list for GROMACS users >> > > >> > >> Dear All > >> Hi.. > >> This is in regard to your previously replied mail regarding the use of > >> GROMOS96 or OPLS-AA or AMBER force field. > >> As you said it depends upon the users taste which one to use. This > >> means that the three on a broad manner should give convergence of > >> the analyzed data set. > >> Infact from my simulation runs using oplss-aa and gromos96, I didn't > >> found that. I tried using the GROMOS96 and opls-aa force field on my > >> small peptides for a period of 20ns and found that with opls-aa even > >> the phi-psi combination of the individual amino acids were incorrect. > >> Actually this always puzzled me to make a choice for the Force field. > >> The rest of the script was unchanged for the two runs. > >> Could you please comment on the above results? Is there any way really > >> to judge which force field is to be chosen for particular type of > >> analysis? > >> Best regards > >> Nav > >> > > > what do you mean with incorrect? your question is quite vague. > > the g_rama program works only for GROMOS like force fields unfortunately > but that doesn't mean the phi/psi are wrong. Could you please give more detail why g_rama program works only for GROMOS like force field? To my understanding, the reason to get different values of phi/psi by using g_rama or g_angle is that the definition of phi/psi in g_rama is not in a conventional way. If we define phi/psi in the same way as g_rama, I believe g_angle will give the same answer. No matter which force field is used, these two methods will give different values. Is my understanding correct? All the best! Dongsheng > What would be the "correct" > result anyway? Maybe your peptide unfolds. > From asillanp at csc.fi Thu Sep 14 17:10:41 2006 From: asillanp at csc.fi (=?ISO-8859-1?Q?Atte_Sillanp=E4=E4?=) Date: Thu, 14 Sep 2006 18:10:41 +0300 (EEST) Subject: [gmx-users] short range nonbondeds = 0 in power4 In-Reply-To: <45096485.3080603@xray.bmc.uu.se> References: <45096485.3080603@xray.bmc.uu.se> Message-ID: On Thu, 14 Sep 2006, David van der Spoel wrote: >> I've run into a mysterious problem. The versions 3.3. and 3.3.1 compile and >> execute, but the short range coulomb and LJ energies come out as zero when >> using the mpi-version. Serial code works ok (mpi version gives zero if run >> using just one cpu). No errors, no warnings. ... > if you suspect PME, then try running without it. Hi again, the short range energies come out as zero with all electrostatic methods cut-off, PME, shift. But only the short range. Other components get some numbers (and you _can_ continue the simulation for at least thousands of steps). Cheers, Atte > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From navratna.vajpai at unibas.ch Thu Sep 14 18:08:09 2006 From: navratna.vajpai at unibas.ch (Navratna Vajpai) Date: Thu, 14 Sep 2006 18:08:09 +0200 Subject: [gmx-users] Hi... In-Reply-To: <45096596.2010302@xray.bmc.uu.se> References: <202973AA-D3F2-40A0-A83A-53DA379505D2@unibas.ch> <71040B4B-C03C-4A71-88D0-3DB34FF08A7E@unibas.ch> <45095AEF.3070100@xray.bmc.uu.se> <445B8F54-B28E-4C16-A81C-4D89A83D9854@unibas.ch> <45096596.2010302@xray.bmc.uu.se> Message-ID: <32E0D60A-F3E5-432E-9777-607541B0D76D@unibas.ch> As suggested by you I tried using the g_angle. But got tucked. It asks for a .ndx file. I tried making it using mk_angndx but gave me an error when i used the option -type phi-psi. Although it worked well when I used the option dihedral instead of phi-psi. The .ndx file has strange nomenclature which i didn't followed. [ Phi=180.0_2_33.5 ] or [ Phi=0.0_3_3.77 ] Please suggest. As you said problem with the analysis program g_rama. I looked for g_rama as well as g_chi .. its mentioned in the g_chi option that the phi psi calculation are different from the conventional calculations. Instead of C'(i-1)-Ni-CAi-C'i , H-N-CA-C' is used and similarly its different for the psi as well. But it also states that it is different from the g_rama. I was wondering what other atoms are taken for the phi-psi calculations? Best regards Nav On Sep 14, 2006, at 4:22 PM, David van der Spoel wrote: > Navratna Vajpai wrote: >> Sorry for not so explicitly explaining the things.. Here it goes >> I have a nona peptide and I ran a MD of 20ns using OPLS-AA force >> field. when I used the OPLS-AA the phi angles came out to be -ve >> for three of the amino acids. which is stericaly not allowed. But >> when I ran it using GROMOS I found all the phi-psi combinations >> with a negative phi value distribution. But now I am lost as you >> have said it works only for GROMOS like force field. Why? > > problem in the anaysis program (assuming you used g_rama). please > use g_angle. > >> and if that so I have got -ve phi distribution for the other phi- >> psi plots. My other question remained unanswered even now. Is >> there any way really to judge which force field is to be chosen >> for particular type of analysis? >> Best regards Thanks >> > > what do you mean with -ve ? > > force field can be evaluated in many ways. > > Start by checking this paper and references in them: > > Hydration thermodynamic properties of amino Acid analogues: a > systematic comparison of biomolecular force fields and water models. > > * Hess B, > * van der Vegt NF. > > J Phys Chem B Condens Matter Mater Surf Interfaces Biophys. 2006 > Sep 7;110(35):17616-26. > > -- > David. > ______________________________________________________________________ > __ > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > ++++ > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php ******************************************* Navratna Vajpai Ph. D student in Prof. Grzesiek's laboratory Department of Structural Biology Biozentrum, University of Basel Klingelbergstrasse 70, CH-4056 Basel, Switzerland. Phone- +41 61 267 2080(O) +41 78 744 0810(M) navratna.vajpai at unibas.ch -------------- next part -------------- An HTML attachment was scrubbed... URL: From nsapay at ucalgary.ca Thu Sep 14 19:37:44 2006 From: nsapay at ucalgary.ca (Nicolas SAPAY) Date: Thu, 14 Sep 2006 11:37:44 -0600 (MDT) Subject: [gmx-users] CHARMM force field implementation in Gromacs : In-Reply-To: <36227.150.203.145.27.1158112340.squirrel@sqmail.anu.edu.au> References: <33710.136.159.234.195.1158109780.squirrel@136.159.234.195> <36227.150.203.145.27.1158112340.squirrel@sqmail.anu.edu.au> Message-ID: <35551.136.159.234.195.1158255464.squirrel@136.159.234.195> Thanks for your answers (I had forgotten this comment in the script). The problem is that most of dihedral with multiplicity n >= 6 don't come alone. For exemple in Arg : HD1 HE | | | // --CG--CD--NE--CZ | | \ HD2 is defined by 6 dihedral with n>=6 (CG-CD-NE-HE, ..., HD2-CD-NE-CZ)> They are all of the same type (X-CT2-CT2-X). So, if I understand well, the result should be OK since, for example, CG-CD-NE-HE and CG-CD-NE-CZ are not a combination of different type of dihedrals with n >= 6. The problems happen when a combination of different types of dihedral are used (for example if CG-CD-NE-HE is of type A and CG-CD-NE-CZ is of type B). In this case, one possibility is to hack the Gromacs code by allowing a 6th Ryckaert-Bellemans parameter (?) Cheers Nico >> Hello, >> >> I have noticed that both in the Yuguang Mu's and the Mark Abraham's >> work, >> the periodic parameters of dihedral angles have been converted into >> Ryckaert-Bellemans ones. I have tried to find more info about this in >> the >> CHARMM and Gromacs documentations but I have not found much. Why >> exactly >> this conversion should be done since the periodic potential is >> implemented >> in both force fields? My problem is that several dihedral angles cannot >> be >> easily converted in RB parameters since their multiplicities is equal to >> 6 >> and the RB potential implemetation is limited to 5 constants. > > To quote my own code comment, > > "# We need some elaborate functionality to convert the CHARMM dihedral > type > # of k * (1 + cos(n * xi - delta ) ) functions summed over n into > something > # GROMACS can implement. While the above functional form exists in > # GROMACS, you can't have more than one function of this type, and > # CHARMM has a number of dihedral interactions that require more than > # one such function. However for delta = 0 or pi and n <= 5, then the > above > # cosine function can be expanded in powers of cos xi, and the > coefficients > # of the expansion can be summed in this conversion and presented to > # GROMACS as a ready-made Ryckaert-Bellemans dihedral. In practice, this > # works because CHARMM only uses such delta and n values for atom type > # combinations that need multiple functions of the above form. Warnings > # are issued when delta is some other value, and the algorithm dies if > # n is > 6. In order to simplify GROMACS logfile output so that it only > # has to report one sort of dihedral term for most simulations, all > # dihedral terms with n <= 5 are expressed as R-B, even when not > necessary. > # Dihedrals with n=6 are left in periodic form, since it is not possible > # to convert these to R-B form when the summation is limited to the > # fifth power of cos xi." > > So if you have a single dihedral over a set of atoms that has n>=6 then > you can leave it in periodic form and the only cost is that you have to > remember that the output will likely have both periodic and R-B > dihedrals. > If you have one such a dihedral in combination with others n<6 then you > can use a combination of periodic and R-B. If you have multiple dihedrals > with n>=6 you will need to hack the source code, except in some trivial > cases, perhaps. > > Mark > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > From akshay17 at olemiss.edu Thu Sep 14 20:48:11 2006 From: akshay17 at olemiss.edu (Akshay Patny) Date: Thu, 14 Sep 2006 13:48:11 -0500 Subject: [gmx-users] DPPC Bilayer Size Message-ID: <001f01c6d82e$54825280$8aa74a82@Plasma> Hi All I am trying to simulate a GPCR protein belonging to the rhodopsin family with amino acid length of 320 residues. Also, I would be using the pre-hydrated DPPC bilayer, can somebody suggest that for a GPCR protein of roughly 320 aa, how big DPPC bilayer would be appropriate to use e.g. 128 DPPC bilayer is available from Peter Tieleman's website http://moose.bio.ucalgary.ca/index.php?page=Main . Thanks Akshay Patny Graduate Research Assistant Faser Hall 417, Department of Medicinal Chemistry Research Institute of Pharmaceutical Sciences University of Mississippi University, MS 38677 E-mail: akshay17 at olemiss.edu Tel: 662-915-1286 (office); Web: www.olemiss.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From spoel at xray.bmc.uu.se Thu Sep 14 22:02:28 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Thu, 14 Sep 2006 13:02:28 -0700 Subject: [gmx-users] CHARMM force field implementation in Gromacs : In-Reply-To: <35551.136.159.234.195.1158255464.squirrel@136.159.234.195> References: <33710.136.159.234.195.1158109780.squirrel@136.159.234.195> <36227.150.203.145.27.1158112340.squirrel@sqmail.anu.edu.au> <35551.136.159.234.195.1158255464.squirrel@136.159.234.195> Message-ID: <4509B554.5020802@xray.bmc.uu.se> Nicolas SAPAY wrote: > Thanks for your answers (I had forgotten this comment in the script). > > The problem is that most of dihedral with multiplicity n >= 6 don't come > alone. For exemple in Arg : > > HD1 HE > | | | // > --CG--CD--NE--CZ > | | \ > HD2 > > is defined by 6 dihedral with n>=6 (CG-CD-NE-HE, ..., HD2-CD-NE-CZ)> They > are all of the same type (X-CT2-CT2-X). So, if I understand well, the > result should be OK since, for example, CG-CD-NE-HE and CG-CD-NE-CZ are > not a combination of different type of dihedrals with n >= 6. > > The problems happen when a combination of different types of dihedral are > used (for example if CG-CD-NE-HE is of type A and CG-CD-NE-CZ is of type > B). In this case, one possibility is to hack the Gromacs code by allowing > a 6th Ryckaert-Bellemans parameter (?) > > Cheers > > Nico > > >>> Hello, >>> >>> I have noticed that both in the Yuguang Mu's and the Mark Abraham's >>> work, >>> the periodic parameters of dihedral angles have been converted into >>> Ryckaert-Bellemans ones. I have tried to find more info about this in >>> the >>> CHARMM and Gromacs documentations but I have not found much. Why >>> exactly >>> this conversion should be done since the periodic potential is >>> implemented >>> in both force fields? My problem is that several dihedral angles cannot >>> be >>> easily converted in RB parameters since their multiplicities is equal to >>> 6 >>> and the RB potential implemetation is limited to 5 constants. >> To quote my own code comment, >> >> "# We need some elaborate functionality to convert the CHARMM dihedral >> type >> # of k * (1 + cos(n * xi - delta ) ) functions summed over n into >> something >> # GROMACS can implement. While the above functional form exists in >> # GROMACS, you can't have more than one function of this type, and >> # CHARMM has a number of dihedral interactions that require more than >> # one such function. However for delta = 0 or pi and n <= 5, then the >> above >> # cosine function can be expanded in powers of cos xi, and the >> coefficients >> # of the expansion can be summed in this conversion and presented to >> # GROMACS as a ready-made Ryckaert-Bellemans dihedral. In practice, this >> # works because CHARMM only uses such delta and n values for atom type >> # combinations that need multiple functions of the above form. Warnings >> # are issued when delta is some other value, and the algorithm dies if >> # n is > 6. In order to simplify GROMACS logfile output so that it only >> # has to report one sort of dihedral term for most simulations, all >> # dihedral terms with n <= 5 are expressed as R-B, even when not >> necessary. >> # Dihedrals with n=6 are left in periodic form, since it is not possible >> # to convert these to R-B form when the summation is limited to the >> # fifth power of cos xi." >> >> So if you have a single dihedral over a set of atoms that has n>=6 then >> you can leave it in periodic form and the only cost is that you have to >> remember that the output will likely have both periodic and R-B >> dihedrals. >> If you have one such a dihedral in combination with others n<6 then you >> can use a combination of periodic and R-B. If you have multiple dihedrals >> with n>=6 you will need to hack the source code, except in some trivial >> cases, perhaps. >> >> Mark You can add multiple dihedrals with identical atoms in the top file, don't know about the rtp file. >> >> _______________________________________________ >> gmx-users mailing list gmx-users at gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-request at gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> > > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From spoel at xray.bmc.uu.se Thu Sep 14 22:10:57 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Thu, 14 Sep 2006 13:10:57 -0700 Subject: Fwd: [gmx-users] Hi... In-Reply-To: <1158245212.19729.8.camel@pampas.chem.purdue.edu> References: <202973AA-D3F2-40A0-A83A-53DA379505D2@unibas.ch> <71040B4B-C03C-4A71-88D0-3DB34FF08A7E@unibas.ch> <45095AEF.3070100@xray.bmc.uu.se> <1158245212.19729.8.camel@pampas.chem.purdue.edu> Message-ID: <4509B751.8080805@xray.bmc.uu.se> Dongsheng Zhang wrote: > On Thu, 2006-09-14 at 06:36 -0700, David van der Spoel wrote: >> Navratna Vajpai wrote: >>> Hi all.. >>> I wrote this mail yesterday. But could not receive any reply till now. >>> So if someone can suggest something about it. That would be nice. >>> Best regards >>> Nav >>> >>> Begin forwarded message: >>> >>>> *From: *Navratna Vajpai >>> > >>>> *Date: *September 13, 2006 10:32:21 AM GMT+02:00 >>>> *To: *Discussion list for GROMACS users >>> > >>>> *Subject: **[gmx-users] Hi...* >>>> *Reply-To: *Discussion list for GROMACS users >>> > >>>> >>>> Dear All >>>> Hi.. >>>> This is in regard to your previously replied mail regarding the use of >>>> GROMOS96 or OPLS-AA or AMBER force field. >>>> As you said it depends upon the users taste which one to use. This >>>> means that the three on a broad manner should give convergence of >>>> the analyzed data set. >>>> Infact from my simulation runs using oplss-aa and gromos96, I didn't >>>> found that. I tried using the GROMOS96 and opls-aa force field on my >>>> small peptides for a period of 20ns and found that with opls-aa even >>>> the phi-psi combination of the individual amino acids were incorrect. >>>> Actually this always puzzled me to make a choice for the Force field. >>>> The rest of the script was unchanged for the two runs. >>>> Could you please comment on the above results? Is there any way really >>>> to judge which force field is to be chosen for particular type of >>>> analysis? >>>> Best regards >>>> Nav >>>> >> >> what do you mean with incorrect? your question is quite vague. >> >> the g_rama program works only for GROMOS like force fields unfortunately >> but that doesn't mean the phi/psi are wrong. > > Could you please give more detail why g_rama program works only for > GROMOS like force field? To my understanding, the reason to get > different values of phi/psi by using g_rama or g_angle is that the > definition of phi/psi in g_rama is not in a conventional way. If we > define phi/psi in the same way as g_rama, I believe g_angle will give > the same answer. No matter which force field is used, these two methods > will give different values. Is my understanding correct? > because atom names are hardcoded. if you give g_angle the right definitions in the index file it will work correctly. > > All the best! > > > Dongsheng > > >> What would be the "correct" >> result anyway? Maybe your peptide unfolds. > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From spoel at xray.bmc.uu.se Thu Sep 14 22:13:01 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Thu, 14 Sep 2006 13:13:01 -0700 Subject: [gmx-users] short range nonbondeds = 0 in power4 In-Reply-To: References: <45096485.3080603@xray.bmc.uu.se> Message-ID: <4509B7CD.5050802@xray.bmc.uu.se> Atte Sillanp?? wrote: > On Thu, 14 Sep 2006, David van der Spoel wrote: > >>> I've run into a mysterious problem. The versions 3.3. and 3.3.1 >>> compile and execute, but the short range coulomb and LJ energies come >>> out as zero when using the mpi-version. Serial code works ok (mpi >>> version gives zero if run using just one cpu). No errors, no warnings. > > ... > >> if you suspect PME, then try running without it. > > Hi again, > > the short range energies come out as zero with all electrostatic methods > cut-off, PME, shift. But only the short range. Other components get some > numbers (and you _can_ continue the simulation for at least thousands of > steps). > can you try a small water box on one processor? just to eliminate problems. if you can simulate, that means the forces are correct (or zero too...) try printing the forces in other words. just do one step with all output turned on. > Cheers, > > Atte > >> -- >> David. >> ________________________________________________________________________ >> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, >> Dept. of Cell and Molecular Biology, Uppsala University. >> Husargatan 3, Box 596, 75124 Uppsala, Sweden >> phone: 46 18 471 4205 fax: 46 18 511 755 >> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From dong at pampas.chem.purdue.edu Thu Sep 14 22:20:17 2006 From: dong at pampas.chem.purdue.edu (Dongsheng Zhang) Date: Thu, 14 Sep 2006 16:20:17 -0400 Subject: Fwd: [gmx-users] Hi... In-Reply-To: <4509B751.8080805@xray.bmc.uu.se> References: <202973AA-D3F2-40A0-A83A-53DA379505D2@unibas.ch> <71040B4B-C03C-4A71-88D0-3DB34FF08A7E@unibas.ch> <45095AEF.3070100@xray.bmc.uu.se> <1158245212.19729.8.camel@pampas.chem.purdue.edu> <4509B751.8080805@xray.bmc.uu.se> Message-ID: <1158265218.19729.13.camel@pampas.chem.purdue.edu> On Thu, 2006-09-14 at 13:10 -0700, David van der Spoel wrote: > Dongsheng Zhang wrote: > > On Thu, 2006-09-14 at 06:36 -0700, David van der Spoel wrote: > >> Navratna Vajpai wrote: > >>> Hi all.. > >>> I wrote this mail yesterday. But could not receive any reply till now. > >>> So if someone can suggest something about it. That would be nice. > >>> Best regards > >>> Nav > >>> > >>> Begin forwarded message: > >>> > >>>> *From: *Navratna Vajpai >>>> > > >>>> *Date: *September 13, 2006 10:32:21 AM GMT+02:00 > >>>> *To: *Discussion list for GROMACS users >>>> > > >>>> *Subject: **[gmx-users] Hi...* > >>>> *Reply-To: *Discussion list for GROMACS users >>>> > > >>>> > >>>> Dear All > >>>> Hi.. > >>>> This is in regard to your previously replied mail regarding the use of > >>>> GROMOS96 or OPLS-AA or AMBER force field. > >>>> As you said it depends upon the users taste which one to use. This > >>>> means that the three on a broad manner should give convergence of > >>>> the analyzed data set. > >>>> Infact from my simulation runs using oplss-aa and gromos96, I didn't > >>>> found that. I tried using the GROMOS96 and opls-aa force field on my > >>>> small peptides for a period of 20ns and found that with opls-aa even > >>>> the phi-psi combination of the individual amino acids were incorrect. > >>>> Actually this always puzzled me to make a choice for the Force field. > >>>> The rest of the script was unchanged for the two runs. > >>>> Could you please comment on the above results? Is there any way really > >>>> to judge which force field is to be chosen for particular type of > >>>> analysis? > >>>> Best regards > >>>> Nav > >>>> > >> > >> what do you mean with incorrect? your question is quite vague. > >> > >> the g_rama program works only for GROMOS like force fields unfortunately > >> but that doesn't mean the phi/psi are wrong. > > > > Could you please give more detail why g_rama program works only for > > GROMOS like force field? To my understanding, the reason to get > > different values of phi/psi by using g_rama or g_angle is that the > > definition of phi/psi in g_rama is not in a conventional way. If we > > define phi/psi in the same way as g_rama, I believe g_angle will give > > the same answer. No matter which force field is used, these two methods > > will give different values. Is my understanding correct? > > > because atom names are hardcoded. So you mean, atom names in g_rama is consistent with gromos like FF, not others. If so, could you please add this documentation in g_rama -h. Thank you very much for your clarification. All the best! Dongsheng > if you give g_angle the right > definitions in the index file it will work correctly. > > > > All the best! > > > > > > Dongsheng > > > > > >> What would be the "correct" > >> result anyway? Maybe your peptide unfolds. > > > > _______________________________________________ > > gmx-users mailing list gmx-users at gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-request at gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > From J.F.Hanna at warwick.ac.uk Thu Sep 14 23:10:18 2006 From: J.F.Hanna at warwick.ac.uk (Joanne Hanna) Date: Thu, 14 Sep 2006 22:10:18 +0100 Subject: [gmx-users] Question about use of tpbconv Message-ID: Hi I have a quick question. When you use tpbconv to continue runs what exactly is taken from the *.edr and *.trr files? For instance if I have to run my simulation in short batches of 1ns is it sufficient to just use the run3 files to continue the run (2ns-3ns) or should thr run1, run2 and run3 files by concatenated and then a run4 file generated using the complete edr and trr files. Thanks Jo Joanne Hanna Department of Chemistry University of Warwick Coventry CV4 7AL (02476) 574623 J.F.Hanna at warwick.ac.uk From Mark.Abraham at anu.edu.au Thu Sep 14 23:53:54 2006 From: Mark.Abraham at anu.edu.au (Mark Abraham) Date: Fri, 15 Sep 2006 07:53:54 +1000 Subject: [gmx-users] Question about use of tpbconv In-Reply-To: References: Message-ID: <4509CF72.3060008@anu.edu.au> Joanne Hanna wrote: > Hi > > I have a quick question. When you use tpbconv to continue runs what exactly is taken from the *.edr and *.trr files? For instance if I have to run my simulation in short batches of 1ns is it sufficient to just use the run3 files to continue the run (2ns-3ns) or should thr run1, run2 and run3 files by concatenated and then a run4 file generated using the complete edr and trr files. Exactly what gets taken will vary a bit with the kind of simulation, but only information from the last step is pertinent, and only that gets used. In a very real sense, with positions and momenta and Newton's Laws known, the system doesn't need "memory" in order to determine the next time step. You can verify that by starting a simulation with "run3" and another with a concatenation of runs 1-3. Unless the concatenation has involved some lossy conversion of numbers from one format to another, the final step will be identical and the subsequent simulation identical. Multiple time-step integration would be a slightly different story, of course. Mark From toma0052 at umn.edu Fri Sep 15 00:04:32 2006 From: toma0052 at umn.edu (toma0052) Date: Thu, 14 Sep 2006 17:04:32 CDT Subject: [gmx-users] Surface Tension Calculation Message-ID: <200609142204.k8EM4WxE011795@vendetta.software.umn.edu> Hi, I posted a question a few days ago regarding the calculation of the surface tension of a lipid bilayer in Gromacs. The response that I got was to use the option "#Surf*SurfTens" in g_energy. I am not really sure how to do this. I have looked at the g-energy file in Gromacs, and I don't see any option that is "#Surf*SurfTens". Maybe the file name is wrong, or I am running an older version of Gromacs or something. Let me know if is there is a way to calculate the surface tension of a lipid bilayer within the Gromacs program, or if it is necessary for me to modify the code. (The more detailed the better. I am new to Gromacs) Thanks, Mike Tomasini From asillanp at csc.fi Fri Sep 15 00:08:30 2006 From: asillanp at csc.fi (=?ISO-8859-1?Q?Atte_Sillanp=E4=E4?=) Date: Fri, 15 Sep 2006 01:08:30 +0300 (EEST) Subject: [gmx-users] short range nonbondeds = 0 in power4 In-Reply-To: <4509B7CD.5050802@xray.bmc.uu.se> References: <45096485.3080603@xray.bmc.uu.se> <4509B7CD.5050802@xray.bmc.uu.se> Message-ID: On Thu, 14 Sep 2006, David van der Spoel wrote: > Atte Sillanp?? wrote: >> On Thu, 14 Sep 2006, David van der Spoel wrote: >> >>>> I've run into a mysterious problem. The versions 3.3. and 3.3.1 compile >>>> and execute, but the short range coulomb and LJ energies come out as zero >>>> when using the mpi-version. Serial code works ok (mpi version gives zero >>>> if run using just one cpu). No errors, no warnings. >> >> ... >> >>> if you suspect PME, then try running without it. >> >> Hi again, >> >> the short range energies come out as zero with all electrostatic methods >> cut-off, PME, shift. But only the short range. Other components get some >> numbers (and you _can_ continue the simulation for at least thousands of >> steps). >> > > can you try a small water box on one processor? > just to eliminate problems. if you can simulate, that means the forces are > correct (or zero too...) try printing the forces in other words. > just do one step with all output turned on. Hi, tried that. Forces are almost zero in a small water system (4 first molecules of spc216.gro) as calculated with mdrun_mpi using one processor. With the serial version I get bigger values. I then enlarged the box and increased electrostatics and vdw cutoffs (no PME) to 3 nm so that all atoms feel short range interactions. Now if I compare the forces they are identical for the first 13 atoms (and the x-component for the 14th) and then they differ as shown below. Here are the outputs from veloc.xvg (g_traj -ov ) for the mdrun_mpi (one step, no initial velocities): 0.000000000 -0.000000596 -0.000000834 0.000000000 0.000014305 -0.000000834 0.000000000 0.000014305 -0.000000834 0.000000000 -0.000000596 -0.000000834 0.000000000 -0.000000596 -0.000000834 0.000000000 -0.000000596 -0.000000834 0.000000000 0.000001267 -0.000000834 0.000000000 -0.000008047 -0.000000834 0.000000000 -0.000009909 -0.000000834 0.000000000 -0.000000596 -0.000000834 0.000000000 -0.000000596 0.000058771 0.000000000 -0.000000596 -0.000000834 0.001000000 -0.000002319 0.000021988 0.000000730 -0.000017221 0.000021988 0.000000730 -0.000002319 0.000021988 0.000008180 0.000042384 -0.000037617 0.000000730 -0.000121529 -0.000067419 0.000000730 0.000057285 -0.000007814 0.000000730 -0.000002319 0.000021988 0.000000730 0.000474518 -0.000007814 -0.000058875 -0.000002319 0.000021988 0.000000730 -0.000061924 0.000021988 0.000000730 -0.000121529 0.000021988 0.000000730 0.000116890 -0.000454849 and for mdrun, serial version: 0.000000000 -0.000000596 -0.000000834 0.000000000 0.000014305 -0.000000834 0.000000000 0.000014305 -0.000000834 0.000000000 -0.000000596 -0.000000834 0.000000000 -0.000000596 -0.000000834 0.000000000 -0.000000596 -0.000000834 0.000000000 0.000001267 -0.000000834 0.000000000 -0.000008047 -0.000000834 0.000000000 -0.000009909 -0.000000834 0.000000000 -0.000000596 -0.000000834 0.000000000 -0.000000596 0.000058771 0.000000000 -0.000000596 -0.000000834 0.001000000 0.000445691 0.000485396 -0.000728320 0.003858060 -0.001481560 0.007869650 -0.007034690 -0.000647092 -0.000296186 0.000058261 -0.000170255 -0.000072669 -0.001506360 0.001558280 0.000881006 -0.001148730 0.002094720 0.000404169 -0.000046048 0.000485396 -0.000668715 0.000430790 -0.003686930 0.005530170 -0.001476560 -0.006100920 0.007437520 -0.000165257 -0.000408674 0.000404169 0.000609603 0.001498670 -0.002456850 0.001622880 0.000545001 The difference being: 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000448010 0.000463408 -0.000729050 0.003875281 -0.001503548 0.007868920 -0.007032371 -0.000669080 -0.000304366 0.000015876 -0.000132638 -0.000073398 -0.001384831 0.001625699 0.000880276 -0.001206015 0.002102534 0.000403439 -0.000043728 0.000463408 -0.000669445 -0.000043728 -0.003679116 0.005589045 -0.001474241 -0.006122908 0.007436790 -0.000103333 -0.000430662 0.000403439 0.000731132 0.001476682 -0.002457580 0.001505990 0.000999850 Something starts to go wrong after the first few atoms? Also if I reduce the cutoffs to 0.1 nm, I get short range nonbondeds as zero in both serial and parallel and also other energies identical. These are the forces without any short range forces (cutoff 0.1 nm): 0.000000000 -0.000000596 -0.000000834 0.000000000 0.000014305 -0.000000834 0.000000000 0.000014305 -0.000000834 0.000000000 -0.000000596 -0.000000834 0.000000000 -0.000000596 -0.000000834 0.000000000 -0.000000596 -0.000000834 0.000000000 0.000001267 -0.000000834 0.000000000 -0.000008047 -0.000000834 0.000000000 -0.000009909 -0.000000834 0.000000000 -0.000000596 -0.000000834 0.000000000 -0.000000596 0.000058771 0.000000000 -0.000000596 -0.000000834 0.001000000 -0.000002319 0.000021988 0.000000730 -0.000017221 0.000021988 0.000000730 -0.000002319 0.000021988 0.000008180 0.000042384 -0.000037617 0.000000730 -0.000121529 -0.000067419 0.000000730 0.000057285 -0.000007814 0.000000730 -0.000002319 0.000021988 0.000000730 0.000474518 -0.000007814 -0.000058875 -0.000002319 0.000021988 0.000000730 -0.000061924 0.000021988 0.000000730 -0.000121529 0.000021988 0.000000730 0.000116890 -0.000454849 Cheers, Atte > > >> Cheers, >> >> Atte >> >>> -- >>> David. >>> ________________________________________________________________________ >>> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, >>> Dept. of Cell and Molecular Biology, Uppsala University. >>> Husargatan 3, Box 596, 75124 Uppsala, Sweden >>> phone: 46 18 471 4205 fax: 46 18 511 755 >>> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se >>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> _______________________________________________ >> gmx-users mailing list gmx-users at gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please don't post (un)subscribe requests to the list. Use the www interface >> or send it to gmx-users-request at gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ From nsapay at ucalgary.ca Fri Sep 15 00:31:20 2006 From: nsapay at ucalgary.ca (Nicolas SAPAY) Date: Thu, 14 Sep 2006 16:31:20 -0600 (MDT) Subject: [gmx-users] CHARMM force field : TIP3 LJ parameters In-Reply-To: <35551.136.159.234.195.1158255464.squirrel@136.159.234.195> References: <33710.136.159.234.195.1158109780.squirrel@136.159.234.195> <36227.150.203.145.27.1158112340.squirrel@sqmail.anu.edu.au> <35551.136.159.234.195.1158255464.squirrel@136.159.234.195> Message-ID: <35898.136.159.234.195.1158273080.squirrel@136.159.234.195> Hello everybody, sorry to bother you with my problems another time. I have checked the non-bonded parameters from Yuguang Mu's ffcharmmnb.itp. The parameters for TIP3 atoms (CHARMM's water model) are : c6 c12 HT 1.008 0.000 A 3.1539699357e-09 1.2921281844e-17 OT 15.999 0.000 A 2.4895403920e-03 2.4347673691e-06 I obtain exactly the same thing according to the combination rule #1 and my own version of the charmm ff. The differences happen when the pair HT..OT is combined in [nonbond-params] (using comb-rule #1 and function #1). Yuguang's parameters are : c6 c12 HT OT 1 4.3824474706e-05 1.3719498873e-09 while I obtain : c6 c12 OT HT 1 2.802131e-06 5.608950e-12 according to chapter 5.6.1, the computation should be C_ij^(M) = sqrt(C_i^(M) . C_j^(M)) with M = [0,6]. So, for the OT..HT pair : C_ij(6) = sqrt( 2.490e-03 x 3.154e-09 ) = sqrt( 7.852e-12 ) = 2.802e-06 C_ij(12)= sqrt( 2.435e-06 x 1.292e-17 ) = sqrt( 3.146e-23 ) = 5.609e-12 Has Someone an idea about this difference? Have I missed something? I have checked several other pairs (with or without CHARMM's 1-4 parameters) : the problem seem to be limited to the OT..HT pair cheers Nicolas -- [ Nicolas Sapay Ph.D. ] University of Calgary, Dept. of Biological Sciences 2500 University Dr. NW, Calgary AB, T2N 1N4, Canada Tel: (403) 220-6869 Fax: (403) 289-9311 From Mark.Abraham at anu.edu.au Fri Sep 15 02:05:28 2006 From: Mark.Abraham at anu.edu.au (Mark Abraham) Date: Fri, 15 Sep 2006 10:05:28 +1000 Subject: [gmx-users] CHARMM force field implementation in Gromacs : In-Reply-To: <35551.136.159.234.195.1158255464.squirrel@136.159.234.195> References: <33710.136.159.234.195.1158109780.squirrel@136.159.234.195> <36227.150.203.145.27.1158112340.squirrel@sqmail.anu.edu.au> <35551.136.159.234.195.1158255464.squirrel@136.159.234.195> Message-ID: <4509EE48.1030200@anu.edu.au> Nicolas SAPAY wrote: > Thanks for your answers (I had forgotten this comment in the script). > > The problem is that most of dihedral with multiplicity n >= 6 don't come > alone. For exemple in Arg : > > HD1 HE > | | | // > --CG--CD--NE--CZ > | | \ > HD2 > > is defined by 6 dihedral with n>=6 (CG-CD-NE-HE, ..., HD2-CD-NE-CZ)> They > are all of the same type (X-CT2-CT2-X). So, if I understand well, the > result should be OK since, for example, CG-CD-NE-HE and CG-CD-NE-CZ are > not a combination of different type of dihedrals with n >= 6. Correct. A dihedral is defined by the four atoms, the functional form and the parameters. The energy profile of rotation about the CD-NE bond is a linear combination of however many dihedrals it is, which is a quite different thing. > The problems happen when a combination of different types of dihedral are > used (for example if CG-CD-NE-HE is of type A and CG-CD-NE-CZ is of type > B). In this case, one possibility is to hack the Gromacs code by allowing > a 6th Ryckaert-Bellemans parameter (?) This is not a problem. None of these dihedral functions occupy the same "space", in that (by the above definition) they have a different set of four atoms despite having the same functional form and central atoms. The potential problem comes because the [ dihedraltypes ] section of either the .top file (or the *bon.itp file that is #included) does not allow multiple dihedral functions of the same functional form to apply to the same set of four atom types - grompp just uses the last one defined. As David correctly points out (and I learned something here!), you can define multiple dihedrals of the same form for the same set of four *atoms* (not atom types) in the [ dihedrals ] section of the .top file. You have to read chapter 5 closely to pick that up though (5.6.1 and 5.7.2). So yet another solution to the general problem would be for a script to post-process the CHARMM .top file to "correct" the dihedrals where multiple periodic functions apply to given set of four atom types. Mark From yappik4050 at yahoo.com Fri Sep 15 02:22:12 2006 From: yappik4050 at yahoo.com (Cherry Y. Yates) Date: Thu, 14 Sep 2006 17:22:12 -0700 (PDT) Subject: [gmx-users] periodic boundary condition Message-ID: <20060915002212.27917.qmail@web56914.mail.re3.yahoo.com> Dear gromacs developers and users, I am calculating a nanotube which has periodic boundary condition along one direction. I wonder how to make an itp file for this system. The difficulty lies in describing the bond between two end atoms, e.g., two atoms are bonded in an infinite length system, but are located on the bottom and top of a unit cell. Thanks, Cherry --------------------------------- Get your email and more, right on the new Yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From zhongqiao_hu at nus.edu.sg Fri Sep 15 04:02:46 2006 From: zhongqiao_hu at nus.edu.sg (Hu Zhongqiao) Date: Fri, 15 Sep 2006 10:02:46 +0800 Subject: [gmx-users] Why RMSFs of some protein chains in my system are unreasonably large? Message-ID: <62AAE6335EB82749B7D92E1DFB8B57848BB857@MBX21.stu.nus.edu.sg> Dear all, I finish a 10-ns MD simulations for a system including 16 lysozyme molecule chains, some solvents H2O molecules and 128 Cl- counter ions under PBC. When I use the command to calculate the RMSF of residues as follows: g_rmsf -f ***.xtc -s ***.tpr -o rmsf_res.xvg (I selected 3 for groups) The results showed that 3rd and 14the chain had RMSF 1.2-2nm, which is obviously unreasonable. But compared with other chains, these 2 chains have the basically same peak places. The difference is that RMSFs of residues in these 2 chains are systematically much higher. Is there a bug resulting in a systematic error or any other reasons? Any suggestions are welcome. Thanks, Zhongqiao Hu Dept of Chemical and Biomolecular Engineering National University of Singapore -------------- next part -------------- An HTML attachment was scrubbed... URL: From Dallas.Warren at vcp.monash.edu.au Fri Sep 15 03:41:57 2006 From: Dallas.Warren at vcp.monash.edu.au (Dallas B. Warren) Date: Fri, 15 Sep 2006 11:41:57 +1000 Subject: [gmx-users] Surface Tension Calculation In-Reply-To: <200609142204.k8EM4WxE011795@vendetta.software.umn.edu> Message-ID: <89907EA1DCFB7548A431C13A270F9DD5022EF020@prk-exch-01.vcp.local> > I posted a question a few days ago regarding the > calculation of the surface tension of a lipid bilayer in > Gromacs. The response that I got was to use the option > "#Surf*SurfTens" in g_energy. I am not really sure how to do > this. I have looked at the g-energy file in Gromacs, and I > don't see any option that is "#Surf*SurfTens". Maybe the > file name is wrong, or I am running an older version of > Gromacs or something. Let me know if is there is a way to > calculate the surface tension of a lipid bilayer within the > Gromacs program, or if it is necessary for me to modify the > code. (The more detailed the better. I am new to Gromacs) I case no-one else responds .... by the sound of it, whether the surf term is present within the energy file will depend on the type of pressure coupling you are using. From spoel at xray.bmc.uu.se Fri Sep 15 05:50:58 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Thu, 14 Sep 2006 20:50:58 -0700 Subject: [gmx-users] Why RMSFs of some protein chains in my system are unreasonably large? In-Reply-To: <62AAE6335EB82749B7D92E1DFB8B57848BB857@MBX21.stu.nus.edu.sg> References: <62AAE6335EB82749B7D92E1DFB8B57848BB857@MBX21.stu.nus.edu.sg> Message-ID: <450A2322.4090604@xray.bmc.uu.se> Hu Zhongqiao wrote: > Dear all, > > I finish a 10-ns MD simulations for a system including 16 lysozyme > molecule chains, some solvents H2O molecules and 128 Cl- counter ions > under PBC. When I use the command to calculate the RMSF of residues as > follows: > > g_rmsf -f ***.xtc -s ***.tpr -o rmsf_res.xvg (I selected 3 for groups) > > The results showed that 3rd and 14the chain had RMSF 1.2-2nm, which is > obviously unreasonable. But compared with other chains, these 2 chains > have the basically same peak places. The difference is that RMSFs of > residues in these 2 chains are systematically much higher. Is there a > bug resulting in a systematic error or any other reasons? Any > suggestions are welcome. Thanks, > > Zhongqiao Hu > Dept of Chemical and Biomolecular Engineering > National University of Singapore > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php are all the lysozymes treated as one protein? in that case it might be a PBC artifact. try doing the rmsf per molecule (by running the program 16 times) and then overlaying the result. are you trying to crystallize it? -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From spoel at xray.bmc.uu.se Fri Sep 15 05:56:43 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Thu, 14 Sep 2006 20:56:43 -0700 Subject: [gmx-users] periodic boundary condition In-Reply-To: <20060915002212.27917.qmail@web56914.mail.re3.yahoo.com> References: <20060915002212.27917.qmail@web56914.mail.re3.yahoo.com> Message-ID: <450A247B.7050608@xray.bmc.uu.se> Cherry Y. Yates wrote: > Dear gromacs developers and users, > > I am calculating a nanotube which has periodic boundary condition along > one direction. I wonder how to make an itp file for this system. The > difficulty lies in describing the bond between two end atoms, e.g., two > atoms are bonded in an infinite length system, but are located on the > bottom and top of a unit cell. use x2top and in your mdp file use pbc=full > > Thanks, > > Cherry > > ------------------------------------------------------------------------ > Get your email and more, right on the new Yahoo.com > > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From spoel at xray.bmc.uu.se Fri Sep 15 06:10:57 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Thu, 14 Sep 2006 21:10:57 -0700 Subject: [gmx-users] Surface Tension Calculation In-Reply-To: <200609142204.k8EM4WxE011795@vendetta.software.umn.edu> References: <200609142204.k8EM4WxE011795@vendetta.software.umn.edu> Message-ID: <450A27D1.6080806@xray.bmc.uu.se> toma0052 wrote: > Hi, > I posted a question a few days ago regarding the calculation of the > surface tension of a lipid bilayer in Gromacs. The response that I got was > to use the option "#Surf*SurfTens" in g_energy. I am not really sure how > to do this. I have looked at the g-energy file in Gromacs, and I don't see > any option that is "#Surf*SurfTens". Maybe the file name is wrong, or I am > running an older version of Gromacs or something. Let me know if is there > is a way to calculate the surface tension of a lipid bilayer within the > Gromacs program, or if it is necessary for me to modify the code. (The > more detailed the better. I am new to Gromacs) yes, print the diagonal terms of the pressure tensor, and assuming you surface is normal to the Z-axis you have gamma = (Pzz - (Pxx+Pyy)/2) / Lz where Lz is the box length. If you have two surfaces you have to divide by two. > > Thanks, > Mike Tomasini > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From zzhwise1 at 163.com Fri Sep 15 06:16:57 2006 From: zzhwise1 at 163.com (zzhwise1) Date: Fri, 15 Sep 2006 12:16:57 +0800 (CST) Subject: [gmx-users] is it my mdp's wrong? Message-ID: <450A2939.0000DC.08302@bj163app70.163.com> hi all my system is lb film of 36 c14cooh long chains! my gro and itp wrote correctly,but when i used the l-bfgs to minimize the system ,the grompp show invalid order "moleculetype",when use the MD ,it showed the atom number in gro not the same as in itp? is it my mdp's wrong? -------------- next part -------------- An HTML attachment was scrubbed... URL: From spoel at xray.bmc.uu.se Fri Sep 15 06:19:49 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Thu, 14 Sep 2006 21:19:49 -0700 Subject: [gmx-users] is it my mdp's wrong? In-Reply-To: <450A2939.0000DC.08302@bj163app70.163.com> References: <450A2939.0000DC.08302@bj163app70.163.com> Message-ID: <450A29E5.8020405@xray.bmc.uu.se> zzhwise1 wrote: > hi all > my system is lb film of 36 c14cooh long chains! my gro and itp wrote > correctly,but when i used the l-bfgs to minimize the system ,the grompp > show invalid order "moleculetype",when use the MD ,it showed the atom > number in gro not the same as in itp? > is it my mdp's wrong? no, the topology. > > > > > > > > > 3G ? ? ? ? ??? ? ? ? ? ? ? ? ? ? > ? ? ? ? ? 3G ? ? ? ? ? ? ?280 ? ? ? ? ? ? ? ? ? ? > ? ? ? > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From zzhwise1 at 163.com Fri Sep 15 07:42:45 2006 From: zzhwise1 at 163.com (zzhwise1) Date: Fri, 15 Sep 2006 13:42:45 +0800 (CST) Subject: [gmx-users] mdp wrong Message-ID: <450A3D55.00012B.06163@bj163app53.163.com> hi follow the last problem ,i checked my gro,itp and modifid,but this time ,"invalid command line argument",what's that mean? is still my mdp'wrong?but this mdp that i test well in other gro ,and itp in ffgrom96,and this time ,my forcefield is ffoplsaa,is there any different in the mdp? -------------- next part -------------- An HTML attachment was scrubbed... URL: From cesar.araujo at oulu.fi Fri Sep 15 17:43:11 2006 From: cesar.araujo at oulu.fi (Cesar Araujo) Date: Fri, 15 Sep 2006 08:43:11 -0700 Subject: [gmx-users] Re: gmx-users Digest, Vol 29, Issue 49 References: <20060915002240.36BE724082@xray.bmc.uu.se> Message-ID: <005201c6d8dd$a9b82ef0$83e8e782@mole232131> Hi Joanna, You can use your last *.tpr/trr/edr files to continue a simulation. The only thing to be aware is if the integrity of the last files is conserved. If not (for example after a system crash), you should exclude the last frame in order to avoid inconsistencies. Regards, C?sar.- ----------------------------------------------------------- Cesar Araujo, Lic. of Chemistry Department of Molecular Endocrynology Oulu University Hospital FIN-90029 OYS, OULU, FINLAND phone: +358 8 3155632 e-mail: cesar.araujo at oulu.fi > Message: 1 > Date: Thu, 14 Sep 2006 22:10:18 +0100 > From: "Joanne Hanna" > Subject: [gmx-users] Question about use of tpbconv > To: > Message-ID: > Content-Type: text/plain; charset=US-ASCII > > Hi > > I have a quick question. When you use tpbconv to continue runs what > exactly is taken from the *.edr and *.trr files? For instance if I have to > run my simulation in short batches of 1ns is it sufficient to just use the > run3 files to continue the run (2ns-3ns) or should thr run1, run2 and run3 > files by concatenated and then a run4 file generated using the complete > edr and trr files. > > Thanks > Jo > > Joanne Hanna > Department of Chemistry > University of Warwick > Coventry > CV4 7AL > > (02476) 574623 > J.F.Hanna at warwick.ac.uk > From Dallas.Warren at vcp.monash.edu.au Fri Sep 15 08:20:57 2006 From: Dallas.Warren at vcp.monash.edu.au (Dallas B. Warren) Date: Fri, 15 Sep 2006 16:20:57 +1000 Subject: [gmx-users] mdp wrong In-Reply-To: <450A3D55.00012B.06163@bj163app53.163.com> Message-ID: <89907EA1DCFB7548A431C13A270F9DD5022EF161@prk-exch-01.vcp.local> > follow the last problem ,i checked my gro,itp and modifid,but this time > ,"invalid command line argument",what's that mean? is still my mdp'wrong? > but this mdp that i test well in other gro ,and itp in ffgrom96,and this time > ,my forcefield is ffoplsaa,is there any different in the mdp? It means exactly what it says, there is a command line argument that is incorrect. What is the exact command that you executed to run the script? There is likely a space in the command line text, incorrect letter or something like that. From michael.creel at uab.es Fri Sep 15 09:05:59 2006 From: michael.creel at uab.es (Michael Creel) Date: Fri, 15 Sep 2006 09:05:59 +0200 Subject: [gmx-users] MPI version on parallelknoppix live CD Message-ID: <450A50D7.1000508@uab.es> Hi gromacs users. The there's a new release of the parallelknoppix live CD out that has a single precision, mpi-enabled version of gromacs installed. You can use this CD to set up a cluster and be running gromacs with MPI in about 10 minutes. The gmxdemo/demo file has been modified to allow you to specify the number of nodes to run on. This demo doesn't show much of a speedup, since it's small, but it does show that everything is working. The PK homepage is pareto.uab.es/mcreel/ParallelKnoppix, where you can see a screenshot. If anyone has an example that shows a good speedup, I'd be happy to put it on a future release. Cheers, Michael From svb1 at msstate.edu Fri Sep 15 11:33:07 2006 From: svb1 at msstate.edu (svb1 at msstate.edu) Date: Fri, 15 Sep 2006 04:33:07 -0500 Subject: [gmx-users] Surface Tension Calculation In-Reply-To: <89907EA1DCFB7548A431C13A270F9DD5022EF020@prk-exch-01.vcp.local> References: <89907EA1DCFB7548A431C13A270F9DD5022EF020@prk-exch-01.vcp.local> Message-ID: <1158312787.450a7353f1f95@webmail.msstate.edu> write g_energy 6 0 enter the number 6 is just the corresponding to the surface tension, it can be any one. Quoting "Dallas B. Warren" : > > I posted a question a few days ago regarding the > > calculation of the surface tension of a lipid bilayer in > > Gromacs. The response that I got was to use the option > > "#Surf*SurfTens" in g_energy. I am not really sure how to do > > this. I have looked at the g-energy file in Gromacs, and I > > don't see any option that is "#Surf*SurfTens". Maybe the > > file name is wrong, or I am running an older version of > > Gromacs or something. Let me know if is there is a way to > > calculate the surface tension of a lipid bilayer within the > > Gromacs program, or if it is necessary for me to modify the > > code. (The more detailed the better. I am new to Gromacs) > > I case no-one else responds .... by the sound of it, whether the surf > term is present within the energy file will depend on the type of > pressure coupling you are using. > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > From kobi17 at gmx.de Fri Sep 15 11:33:27 2006 From: kobi17 at gmx.de (kobi) Date: Fri, 15 Sep 2006 11:33:27 +0200 Subject: [gmx-users] The right way of killing Gromacs Message-ID: <450A7367.7000004@gmx.de> Hello, the runtime of our cluster is unfortunately limited. Before mdrun is terminated a USR1 signal is send, but this doesn't cause mdrun to writeout the current frame. Therefore most of the trajectory is lost. I'd like to write a skrip which converts the USR1 sinal to some other signal. The question is, which signal would cause mdrun to write out all data and terminate it afterwards? best regards Jan Neumann From svb1 at msstate.edu Fri Sep 15 11:41:21 2006 From: svb1 at msstate.edu (svb1 at msstate.edu) Date: Fri, 15 Sep 2006 04:41:21 -0500 Subject: [gmx-users] Fatal error: Force field inconsistency In-Reply-To: <1158091046.45071127025ef@webmail.msstate.edu> References: <1158091046.45071127025ef@webmail.msstate.edu> Message-ID: <1158313281.450a75419c0e9@webmail.msstate.edu> Quoting svb1 at msstate.edu: > > > Hello, > I had this error while trying to run a simulation for a small molecule > without > water and bilayer, I have included in the topol.top its parameters taken from > OPLS and its topology, since I did not created the topology with the pdb2gmx > I > did not included the ffoplsa.itp in the topol, however after grompp -norenum > ?debug, and mdrun I got the following message > Fatal error: Force field inconsistency: 1-4 interaction parameters for > atoms 9-10 not the same as for other atoms with the same atom type. > I already checked the [pairs] and found that for the same type of atoms the > parameters are the same . so why is giving me this error?. It doesn't make > sense. > I read in the GROMACS mailing list that including -norenum with grompp, it > make > work but it did not, so what I did was to commented out the 9-10 pair > interaction from [pairs], but still the same error, then I comented out > [pairs] > and all the 1-4 interactions defined in [pairs] in my molecule.itp, and after > grompp and mdrun the system did not complain. > The thing is that now it is calculating the 1-4 interactions from the > molecule > parameters in molecule.itp [which has the parameters and topology], with :[ > defaults ] > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ > 1 1 yes 1.0 0.5 > > because the explicit [pairs ] were comented out due to the Fatal error: Force > field inconsistency. > Can somebody give an advice, some people had this problem posted on the web, > but > I couldn't find the solution for my eventhought we all get the same error. > Thanks, > Sandra > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > From zhongqiao_hu at nus.edu.sg Fri Sep 15 11:47:54 2006 From: zhongqiao_hu at nus.edu.sg (Hu Zhongqiao) Date: Fri, 15 Sep 2006 17:47:54 +0800 Subject: [gmx-users] Re: Why RMSFs of some protein chains in my system are unreasonably large? Message-ID: <62AAE6335EB82749B7D92E1DFB8B57848BB85D@MBX21.stu.nus.edu.sg> > are all the lysozymes treated as one protein? in that case it might be a PBC artifact. try doing the rmsf per molecule (by running the program 16 > times) and then overlaying the result. > are you trying to crystallize it? >David. Thank David. I just found that it was due to jumps in trajectory files. I saw the animation of trajetory file and found some protein molecules jumped from one side to the other side. Thus I produced a new trajectory files using trjconv with option "-pbc nojump" and then calculated RMSF, the result seems OK. So it is a little strange that g_rmsf can not recognize some information about jumps in trajectory file. If it is, could you repair it in the next release? Thanks, Zhongqiao Hu Dept of Chemical and Biomolecular Engi. National Univ. of Singapore -------------- next part -------------- An HTML attachment was scrubbed... URL: From lindahl at cbr.su.se Fri Sep 15 12:05:59 2006 From: lindahl at cbr.su.se (Erik Lindahl) Date: Fri, 15 Sep 2006 12:05:59 +0200 Subject: [gmx-users] The right way of killing Gromacs In-Reply-To: <450A7367.7000004@gmx.de> References: <450A7367.7000004@gmx.de> Message-ID: Hi, mdrun finishes on the next step when receiving TERM, and on the next multiple of nstxout when receiving USR1. On some systems, the USR1/SIGHUP is only sent to the parent MPI program, not the actual mdrun process, and then there isn't much we can do. In your case, try altering the signals in src/kernel/md.c and see if you get it working if you change both signals to cause an exit on the next step. Cheers, Erik On Sep 15, 2006, at 11:33 AM, kobi wrote: > Hello, > > the runtime of our cluster is unfortunately limited. Before mdrun > is terminated a USR1 signal is > send, but this doesn't cause mdrun to writeout the current frame. > Therefore most of the trajectory > is lost. I'd like to write a skrip which converts the USR1 sinal to > some other signal. The question > is, which signal would cause mdrun to write out all data and > terminate it afterwards? > > best regards > Jan Neumann > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php From gmx3 at hotmail.com Fri Sep 15 12:07:34 2006 From: gmx3 at hotmail.com (Berk Hess) Date: Fri, 15 Sep 2006 12:07:34 +0200 Subject: [gmx-users] The right way of killing Gromacs In-Reply-To: <450A7367.7000004@gmx.de> Message-ID: >From: kobi >Reply-To: Discussion list for GROMACS users >To: Discussion list for GROMACS users >Subject: [gmx-users] The right way of killing Gromacs >Date: Fri, 15 Sep 2006 11:33:27 +0200 > >Hello, > >the runtime of our cluster is unfortunately limited. Before mdrun is >terminated a USR1 signal is >send, but this doesn't cause mdrun to writeout the current frame. Therefore >most of the trajectory >is lost. I'd like to write a skrip which converts the USR1 sinal to some >other signal. The question >is, which signal would cause mdrun to write out all data and terminate it >afterwards? mdrun -h explains it. The USR1 signal is what you want, but it should NOT be sent to the master process that spawned the others, and you want to send it in time, that is long enough before the queue time ends so you can reach the next nstvout step. Berk. From qiaobf at gmail.com Fri Sep 15 15:34:35 2006 From: qiaobf at gmail.com (Qiao Baofu) Date: Fri, 15 Sep 2006 15:34:35 +0200 Subject: [gmx-users] Re: question about g_rdf -com & a little mistake on make_ndx Message-ID: <6a91f07b0609150634gf58969agfc9887a1a3ee0d24@mail.gmail.com> Hi, I am using Gromacs 3.3.1. In the help file of make_ndx, it is said that "splitres" is to split group into residues, and "splitat" is to split group into atoms. But after I use them two, I found they are opsite. see the following example > splitres 3 Splitting group 3 'MIL' into atoms > splitat 3 Splitting group 3 'MIL' into residues 2006/9/15, Qiao Baofu < qiaobf at gmail.com>: > > Hi All > > I have 2 questions about using g_rdf -com: > 1. In the manual, it is said that when -com option used, the rdf is > calculated with respect to the center of first group. My question is that, > if i want to calculate the rdf of the COM of two groups, how to do it? > 2. In my mind, for single-atom, the COM should just be the center of it. > Therefore, if I calculate the rdf of two single-atom groups WITH and WITHOUT > -com option, the result should be the same. However, it is not that case. I > calculated the rdf of H-Cl in these two methods, and got quite different > result!! see the attachment. Why? > > > PS: I use gromacs 3.3.1. > > -- > Sincerely yours, > ********************************************** > Baofu Qiao, PhD > Frankfurt Institute for Advanced Studies > Max-von-Laue-Str. 1 > 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 > ********************************************** > > -- Sincerely yours, ********************************************** Baofu Qiao, PhD Frankfurt Institute for Advanced Studies Max-von-Laue-Str. 1 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From diane.fournier at crchul.ulaval.ca Fri Sep 15 16:45:50 2006 From: diane.fournier at crchul.ulaval.ca (Diane Fournier) Date: Fri, 15 Sep 2006 10:45:50 -0400 Subject: [gmx-users] binding free energy calculations on charged ligands Message-ID: Hello all, I'm still trying to get the binding free energy for my ligands, and I now think I will have to do another simulation, since my first one used PME and I didn't record velocities in my trajectory. But first I need some advice, since I can't find a paper which describes unambiguously what I want to do. First, my ligand is charged (carboxylate) ; what is the best (and easiest) method to calculate the binding free energy for charged ligands ? Is MM-PBSA preferable to LIE in that case ? I tried LIE with PME, and I know that you can get the PME contribution by doing a mdrun -rerun with zero charge on all charge groups alternatively. I also understand that this was described in the mail archive, but I can't find the mails in question. Can somebody tell me exactly when those mails were written ? And do the 'standard' settings for PME (as described in the manual) need to be changed ? I understand that the Coul-LR and LJ-LR terms are not produced when rcoulomb = rlist and rvdw = rlist respectively ? Or those are the terms that are calculated in the zero-charged reruns ? Also, what is to be done with the counterions ? Since it does not seem possible to have an equilibrium distribution in a reasonable time (on a ns scale), must I run the simulations without them ? All advice will be very appreciated. Diane -------------- next part -------------- An HTML attachment was scrubbed... URL: From spoel at xray.bmc.uu.se Sat Sep 16 02:45:12 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Fri, 15 Sep 2006 17:45:12 -0700 Subject: [gmx-users] Re: question about g_rdf -com & a little mistake on make_ndx In-Reply-To: <6a91f07b0609150634gf58969agfc9887a1a3ee0d24@mail.gmail.com> References: <6a91f07b0609150634gf58969agfc9887a1a3ee0d24@mail.gmail.com> Message-ID: <450B4918.3070405@xray.bmc.uu.se> Qiao Baofu wrote: > Hi, > I am using Gromacs 3.3.1. In the help file of make_ndx, it is said that > "splitres" is to split group into residues, and "splitat" is to split > group into atoms. But after I use them two, I found they are opsite. see > the following example > > > splitres 3 > Splitting group 3 'MIL' into atoms > > > splitat 3 > Splitting group 3 'MIL' into residues > printing is wrong, result is right. this is already fixed in CVS, but thanks for reporting it anyway. > > > > > 2006/9/15, Qiao Baofu < qiaobf at gmail.com >: > > Hi All > > I have 2 questions about using g_rdf -com: > 1. In the manual, it is said that when -com option used, the rdf is > calculated with respect to the center of first group. My question is > that, if i want to calculate the rdf of the COM of two groups, how > to do it? > 2. In my mind, for single-atom, the COM should just be the center > of it. Therefore, if I calculate the rdf of two single-atom groups > WITH and WITHOUT -com option, the result should be the same. > However, it is not that case. I calculated the rdf of H-Cl in these > two methods, and got quite different result!! see the attachment. Why? > > > PS: I use gromacs 3.3.1. > > -- > Sincerely yours, > ********************************************** > Baofu Qiao, PhD > Frankfurt Institute for Advanced Studies > Max-von-Laue-Str. 1 > 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 > ********************************************** > > > > > -- > Sincerely yours, > ********************************************** > Baofu Qiao, PhD > Frankfurt Institute for Advanced Studies > Max-von-Laue-Str. 1 > 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 > ********************************************** > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chris.neale at utoronto.ca Sat Sep 16 21:26:24 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Sat, 16 Sep 2006 15:26:24 -0400 Subject: [gmx-users] g_mindist -pi (minimum periodic) and dodecahedron Message-ID: <20060916152624.fehmyu7ufxcg0kwk@webmail.utoronto.ca> I have an alanine dipeptide in a box (gromacs-3.3.1). When that box is cubic (3. 3. 3.), g_mindist -pi works as I expect it to (i.e. selecting Protein yields 2.3nm, which is what I would expect for box length minus end to end peptide distance; and selecting a single atom yields 3.0nm). However, when the box type is a rhombic dodecahedron, I get the same g_mindist -pi minimum periodic distance output whether I select "Protein" or just a single atom of that protein. When that box is created by editconf -bt dodecahedron -d 1.110755, I get a box = {3.00000 3.00000 2.12132 0.00000 0.00000 0.00000 0.00000 1.50000 1.50000}, and I get a g_mindist -pi minimum periodic distance of 2.12132 for a selection of the entire protein of just a single atom (or backbone, C-alpha, etc.) For clarification, my protein is not entirely linear and I therefore suggest that this is some type of error. When I further solvate the system and select SOL for g_mindist, the result is 0.136nm. When I select only a single SOL (4 atoms) or only the OW atom within that SOL molecule, I again get 2.12132nm. When I select two solvent residues (8 atoms) I again get 2.12132nm. Thanks for any insight that anybody can offer. One reason that I can't figure this out any further myself is that I don't really understand the transformations involved in triclinic box PBC and VMD won't render all 3 axis positions correctly in periodic display (i.e. there is always an offset in at least one dimension, even when using trjconv -ur) My commands were like this: 1. pdb2gmx -f a.pdb -o a.gro -p a.top -ff oplsaa -water tip4p 2. editconf -f a.gro -o b.gro [(-bt cubic -box 3. 3. 3.) ~OR~ (-bt dodecahedron -d 1.)] 3. make_ndx -f b.gro -o b.ndx < file_selecting_a_single_protein_atom 4. g_mindist -f b.gro -n b.ndx -pi The input pdb file that I used was: ATOM 13 C ALA 2 1.199 4.163 -0.186 1.00 0.00 C ATOM 14 CA ALA 2 1.936 3.140 -1.094 1.00 0.00 C ATOM 15 CB ALA 2 1.931 3.622 -2.546 1.00 0.00 C ATOM 16 H ALA 2 1.473 1.194 -1.741 1.00 0.00 H ATOM 17 HA ALA 2 2.957 3.060 -0.751 1.00 0.00 H ATOM 18 N ALA 2 1.315 1.824 -1.006 1.00 0.00 N ATOM 19 O ALA 2 0.786 3.836 0.926 1.00 0.00 O ATOM 20 1HB ALA 2 2.493 4.541 -2.623 1.00 0.00 H ATOM 21 2HB ALA 2 0.913 3.796 -2.865 1.00 0.00 H ATOM 22 3HB ALA 2 2.381 2.871 -3.177 1.00 0.00 H ATOM 23 C ALA 3 -0.332 7.289 -1.163 1.00 0.00 C ATOM 24 CA ALA 3 0.299 6.426 -0.037 1.00 0.00 C ATOM 25 CB ALA 3 1.277 7.267 0.787 1.00 0.00 C ATOM 26 H ALA 3 1.377 5.531 -1.610 1.00 0.00 H ATOM 27 HA ALA 3 -0.451 6.044 0.639 1.00 0.00 H ATOM 28 N ALA 3 1.015 5.356 -0.716 1.00 0.00 N ATOM 29 O ALA 3 0.349 8.097 -1.795 1.00 0.00 O ATOM 30 1HB ALA 3 1.003 8.309 0.718 1.00 0.00 H ATOM 31 2HB ALA 3 2.278 7.132 0.405 1.00 0.00 H ATOM 32 3HB ALA 3 1.240 6.953 1.819 1.00 0.00 H END ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From chris.neale at utoronto.ca Sun Sep 17 03:16:47 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Sat, 16 Sep 2006 21:16:47 -0400 Subject: [gmx-users] Using ACE and NAC with oplsaa Message-ID: <20060916211647.mjd2hbvpkium88gk@webmail.utoronto.ca> I read over the comments on the mailing list, and found some ways to make the grompp warnings go away while using ACE or NAC terminii, but was not able to understand what the most proper way to do things was. The missing dihedrals are because the CH3 is opls_135 (ACE) or opls_242 (NAC) which are both type "CT" where all other CA atoms are of type CT_2. Based on the following lines from ffoplsaabon.itp: CA N C CT 3 30.28798 -4.81160 -25.47638 0.00000 0.00000 0.00000 ; amides - V1 changed to 2.3 CT C N CT 3 30.28798 -4.81160 -25.47638 0.00000 0.00000 0.00000 ; amides - V1 changed to 2.3 CT_2 C N CT_2 3 30.28798 -4.81160 -25.47638 0.00000 0.00000 0.00000 ; peptide - V1 changed to 2.3 It seems reasonable to me that a CT-C-N-CT_2 RB-dihedral be created with the same values. Therefore I have added the following lines: [ dihedraltypes ] ; i j k l func coefficients CT C N CT_2 3 30.28798 -4.81160 -25.47638 0.00000 0.00000 0.00000 ; For ACE/NAC (Sept2006) adapted from CT_2-N-C-CT_2 parameters with original comment="peptide - V1 changed to 2.3" Added to my topology file after #include "ffoplsaa.itp" and before [ moleculetype ] ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From camilogmx at gmail.com Sun Sep 17 04:07:37 2006 From: camilogmx at gmail.com (Camilo Calderon) Date: Sat, 16 Sep 2006 22:07:37 -0400 Subject: [gmx-users] bond-bond and bond-angle cross terms Message-ID: <7ad2c1660609161907ya90e531tf9102311f4b79cce@mail.gmail.com> Hi all! I am new to the GROMACS-world, and I am mystified. How do I implement the 3 body potentials advertised in sec. 4.2.8 and sec. 4.2.9 of the GROMACS 3.3 manual? Right now I have the following: [ cross_cross_bond ] ;ai aj funct r1e r2e krr [ cross_bond_angle ] ;ai aj ak funct r1e r2e r3e krt when I grompp the topol.top, what I get is a Error, with a complaint "invalid directive", and then a Fatal Error, with the complaint "Incorrect number of parameters - found 5, expected 2 or 4." What is really tough about this is that I've been poring over the source code, trying to decypher what input format ought to be - there is nothing on this either in the Manual, or in the various lists! Thanks a ton! Camilo -------------- next part -------------- An HTML attachment was scrubbed... URL: From zzhwise1 at 163.com Sun Sep 17 04:18:14 2006 From: zzhwise1 at 163.com (zzhwise1) Date: Sun, 17 Sep 2006 10:18:14 +0800 (CST) Subject: [gmx-users] about equilibration and minimization! Message-ID: <450CB066.000017.04865@bj163app91.163.com> i have conformed my system well,then i used the l-bfgs to minimize it for 5000 steps,but it stopped at 245th steps,for system han no change,then ,i used steep but no used,it show "Too many LINCS warnings (10997) - aborting to avoid logfile runaway.
This normally happens when your system is not sufficiently equilibrated,or if you are changing lambda too fast in free energy simulations.
If you know what you are doing you can adjust the lincs warning threshold
in your mdp file, but normally it is better to fix the problem.

---------------------
i want to know what the real equilibration,do the l-bfgs and steep not?
also ,when use MD it show the top and the gro's coordinate not match?why? my gro was correct under other mdp in grompp!
could anyone help me ?
thanks a lot!
-------------- next part -------------- An HTML attachment was scrubbed... URL: From chris.neale at utoronto.ca Sun Sep 17 04:36:00 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Sat, 16 Sep 2006 22:36:00 -0400 Subject: [gmx-users] Re: Using ACE and NAC with oplsaa Message-ID: <20060916223600.kim85q4xzycgos8k@webmail.utoronto.ca> Appologies, two entries are required (the first is for ACE and the second is for NAC): [ dihedraltypes ] ; i j k l func coefficients CT C N CT_2 3 30.28798 -4.81160 -25.47638 0.00000 0.00000 0.00000 For ACE (Sept2006) adapted from CT_2-N-C-CT_2 parameters with original comment="peptide - V1 changed to 2.3" CT_2 C N CT 3 30.28798 -4.81160 -25.47638 0.00000 0.00000 0.00000 For NAC (Sept2006) adapted from CT_2-N-C-CT_2 parameters with original comment="peptide - V1 changed to 2.3" ******************* As an unrelated point: I receive the users list as a coallated email, not as individual emails. Therfore I can't reply directly to an email and can't put a response in the same thread. That isn't ideal (eg. for situations like this where it would be nice for somebody searching later to find a "next in thread"). Is there a way to hack the subject line in order to get a message put into a thread without also having to get all the posts as individual emails? Thanks. ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From chris.neale at utoronto.ca Sun Sep 17 05:05:22 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Sat, 16 Sep 2006 23:05:22 -0400 Subject: [gmx-users] Re: DPPC Bilayer Size Message-ID: <20060916230522.91atemtcyi8skc4c@webmail.utoronto.ca> > I am trying to simulate a GPCR protein belonging to the rhodopsin > family with amino acid length of 320 residues. Also, I would be > using the pre-hydrated DPPC bilayer, can somebody suggest that for a > GPCR protein of > roughly 320 aa, how big DPPC bilayer would be appropriate to use > e.g. 128 DPPC bilayer is available from Peter Tieleman’s > website http://moose.bio.ucalgary.ca/index.php?page=Main . It depends what you are studying I suppose: the lipid or the protein. Certainly you need enough lipid so that one side of the protein doesn't see the other side. An argument could also be made that you don't want any lipids to see both sides of the protein, although I am not sure that this is so essential if your focus is on protein behaviour. As a rough guess, assuming that your protein is roughly globular, I imagine that you should probably use about 300 lipids per leaflet prior to making the hole. There is no way that I can really know, but just in case you have desired this kind of answer... For you to make this estimate yourself, measure the largest diameter in the xy plane (tilted as you expect it to be during the simulation), add 1nm for possible side chain extension and 1.4nm for your rvdw (or whatever you use) and you have a box width that would be the recommended minimum. Compare that to the equilibrated membrane box that you have and get a rough number of lipids/leaflet. However, you will need to be monitoring your run to see that the protein doesn't get bigger in the xy by more than 1nm. I personally like to make the system much too large at first, equilibrate using 3 or 4 cpus in parallel for about 5ns, then analyze to see the distance fluctuations. This allows me to make a safe guess about the minimal box size. With a system so large, technical details like rvdw vs. box size probably won't be an issue. That leaves considerations based on equilibration and cpu hours/ns. 1. There is some information available that a small mass ratio of lipid/protein can lead to reduced ability of the system to reach equilibrium: Molecular Dynamics Simulations of Model Trans-Membrane Peptides in Lipid Bilayers: A Systematic Investigation of Hydrophobic Mismatch Senthil K. Kandasamy and Ronald G. Larson Biophysical journal 2006 This means that although a smaller system will complete more steps in a given period of cpu time, it is not necessarily true that a smaller system will equilibrate faster in a given period of cpu time. 2. If I remember my GPCR biology correctly, they have 7 TMhelicies? That's a huge number of lipids to remove. You want to either be very carefull and test out a couple of methods to remove the lipids (the make_hole version of gromacs or tieleman's groups new expansion/contraction method for example) or have a membrane big enough that if you remove too make lipids from one leaflet, it won't put undue strain on the other leaflet by density values (or you could use the p2sub1 crystal PBC in CHARMM, which I have tried unsuccessfully to implement in gromacs). 3. The size of the required membrane will be minimal when the hydrophobic mismatch is minimal, so getting the correct membrane environment is important. 4. Don't realy on anything that I have said. It's the best that I can do, but really it's just a suggestion. Chris ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From gigo at poczta.ibb.waw.pl Sun Sep 17 12:52:52 2006 From: gigo at poczta.ibb.waw.pl (gigo at poczta.ibb.waw.pl) Date: Sun, 17 Sep 2006 12:52:52 +0200 (CEST) Subject: [gmx-users] openmpi In-Reply-To: <1158207603.4508d87383de6@webmail.utoronto.ca> References: <1158207603.4508d87383de6@webmail.utoronto.ca> Message-ID: Hi, I'm using openmpi on our 24-nodes 2 cores each cluster without any problem so far. I run my jobs under torque and I did not change any of default settings. With my system it scales rather well on 4 nodes, but I have no problems with running more. Grzegorz Wieczorek Department of Bioinformatics Institute of Biochemistry and Biophysics Polish Academy of Sciences ul. Pawinskiego 5a 02-106 Warszawa, Poland On Thu, 14 Sep 2006, chris.neale at utoronto.ca wrote: > Anyone using openmpi for parallel gromacs? If so, how to set the maximum short > tcp length? I have tried some things unsuccessfully which are posted at the open > mpi site: > http://www.open-mpi.org/community/lists/users/2006/09/1864.php > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > From zzhwise1 at 163.com Mon Sep 18 07:30:01 2006 From: zzhwise1 at 163.com (zzhwise1) Date: Mon, 18 Sep 2006 13:30:01 +0800 (CST) Subject: [gmx-users] bond lost! Message-ID: <450E2ED9.00005F.11224@bj163app47.163.com> good everyone i have 2 questions : 1) when i optimized my system of CH3(CH2)13COOH chains with l-bfgs for 5000steps,but it stopped at 467th step,and i found the conformation break,8chains'lost the C-OH bonds,why there was this and what cause this?was this the wrong itp or mdp? 2) when i change the mdp with md,then show the gro atomnumber not incorred with top?why?i still could not find out the reason! can anyone help me? thankS! -------------- next part -------------- An HTML attachment was scrubbed... URL: From Mark.Abraham at anu.edu.au Mon Sep 18 07:37:51 2006 From: Mark.Abraham at anu.edu.au (Mark Abraham) Date: Mon, 18 Sep 2006 15:37:51 +1000 Subject: [gmx-users] bond lost! In-Reply-To: <450E2ED9.00005F.11224@bj163app47.163.com> References: <450E2ED9.00005F.11224@bj163app47.163.com> Message-ID: <450E30AF.8000602@anu.edu.au> zzhwise1 wrote: > good everyone > i have 2 questions : > 1) when i optimized my system of CH3(CH2)13COOH chains with l-bfgs for > 5000steps,but it stopped at 467th step,and i found the conformation > break,8chains'lost the C-OH bonds,why there was this and what cause > this?was this the wrong itp or mdp? Your topology was not correct. Compare the contents of the .top file with the .itp file it was sourced from. > 2) when i change the mdp with md,then show the gro atomnumber not > incorred with top?why?i still could not find out the reason! I can't understand this. You need to describe the problem fully, include contents of small files where appropriate, and quote the feedback you get from the gromacs tools. Or you could employ a mind-reader. I know what's cheaper :-) Mark From jiqing at iccas.ac.cn Mon Sep 18 07:41:43 2006 From: jiqing at iccas.ac.cn (=?gb2312?B?1vfUwiCjuqOp?=) Date: Mon, 18 Sep 2006 13:41:43 +0800 Subject: [gmx-users] The molecule size Message-ID: <000c01c6dae5$1f8e6730$851ae29f@jiqing> Hi: Two melt models were built for polyethylene (PE) and polyvinylmethylether (PVME) melt with PBC condition . The density of both melt model agree with experimenal value well.But when one check the radius of gyration (Rg) of them, both of them were too small to accept as follows. The Rg for PE (C1000) is just 28 angstrom. It means the infinite charaterastic ratio (Cinf) for the polymer is just about 2 which is much smaller than scatter experimental value about 7. The Rg for PVME (C44) melt is about 6.6 angstrom. It means the Cinf for the polymer is just 2.5 which is much smaller than scatter experimental value 8-10. Can these results be accepted? Is there any fault in force field? gromos96a Thanks in advance. ************************************************* Ji Qing Institute of Chemistry, Chinese Academy of Sciences Tel: 0086-10-62562894 ?82618423 ************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From Mark.Abraham at anu.edu.au Mon Sep 18 07:43:06 2006 From: Mark.Abraham at anu.edu.au (Mark Abraham) Date: Mon, 18 Sep 2006 15:43:06 +1000 Subject: [gmx-users] Re: Using ACE and NAC with oplsaa In-Reply-To: <20060916223600.kim85q4xzycgos8k@webmail.utoronto.ca> References: <20060916223600.kim85q4xzycgos8k@webmail.utoronto.ca> Message-ID: <450E31EA.8000809@anu.edu.au> chris.neale at utoronto.ca wrote: > Appologies, two entries are required (the first is for ACE and the > second is for NAC): > > [ dihedraltypes ] > ; i j k l func coefficients > > CT C N CT_2 3 30.28798 -4.81160 -25.47638 > 0.00000 0.00000 0.00000 For ACE (Sept2006) adapted from > CT_2-N-C-CT_2 parameters with original comment="peptide - V1 changed to > 2.3" > > CT_2 C N CT 3 30.28798 -4.81160 -25.47638 > 0.00000 0.00000 0.00000 For NAC (Sept2006) adapted from > CT_2-N-C-CT_2 parameters with original comment="peptide - V1 changed to > 2.3" > > ******************* These entries look correct to me. > As an unrelated point: > > I receive the users list as a coallated email, not as individual > emails. Therfore I can't reply directly to an email and can't put a > response in the same thread. That isn't ideal (eg. for situations like > this where it would be nice for somebody searching later to find a > "next in thread"). Is there a way to hack the subject line in order to > get a message put into a thread without also having to get all the > posts as individual emails? Thanks. No. Threading is not done by interpreting the contents of the subject line, but rather through the use of headers that aren't normally visible in mail readers without the user saying they want to see them. Digests break this. Mark From Mark.Abraham at anu.edu.au Mon Sep 18 07:45:33 2006 From: Mark.Abraham at anu.edu.au (Mark Abraham) Date: Mon, 18 Sep 2006 15:45:33 +1000 Subject: [gmx-users] bond-bond and bond-angle cross terms In-Reply-To: <7ad2c1660609161907ya90e531tf9102311f4b79cce@mail.gmail.com> References: <7ad2c1660609161907ya90e531tf9102311f4b79cce@mail.gmail.com> Message-ID: <450E327D.8090300@anu.edu.au> Camilo Calderon wrote: > Hi all! > I am new to the GROMACS-world, and I am mystified. > How do I implement the 3 body potentials advertised in sec. 4.2.8 and > sec. 4.2.9 of the GROMACS 3.3 manual? > Right now I have the following: > > [ cross_cross_bond ] > ;ai aj funct r1e r2e krr > > > [ cross_bond_angle ] > ;ai aj ak funct r1e r2e r3e krt > > > when I grompp the topol.top, what I get is a Error, with a complaint > "invalid directive", and then a Fatal Error, with the complaint > "Incorrect number of parameters - found 5, expected 2 or 4." What is > really tough about this is that I've been poring over the source code, > trying to decypher what input format ought to be - there is nothing on > this either in the Manual, or in the various lists! The contents of either gmxlib/ifunc.c or kernel/ifunc.c (sorry can't remember which it is) may help you work out how many parameters it needs - text search for CROSS, and then find the definition of the macro that is being used there. Can you give us more detail from the .top file and the error messages grompp returns? Mark From Mark.Abraham at anu.edu.au Mon Sep 18 07:55:52 2006 From: Mark.Abraham at anu.edu.au (Mark Abraham) Date: Mon, 18 Sep 2006 15:55:52 +1000 Subject: [gmx-users] The molecule size In-Reply-To: <000c01c6dae5$1f8e6730$851ae29f@jiqing> References: <000c01c6dae5$1f8e6730$851ae29f@jiqing> Message-ID: <450E34E8.8090001@anu.edu.au> ?? ?? wrote: > Hi: > > Two melt models were built for polyethylene (PE) and > polyvinylmethylether (PVME) melt with PBC condition . > > The density of both melt model agree with experimenal value well.But > when one check the radius of gyration (Rg) of them, both of them were > too small to accept as follows. > > The Rg for PE (C1000) is just 28 angstrom. It means the infinite > charaterastic ratio (Cinf) for the polymer is just about 2 which is much > smaller than scatter experimental value about 7. > > The Rg for PVME (C44) melt is about 6.6 angstrom. It means the Cinf for > the polymer is just 2.5 which is much smaller than scatter experimental > value 8-10. > > Can these results be accepted? > > Is there any fault in force field? gromos96a Usually a garbage result as output means that you had either garbage as input, or garbage for the algorithm. Find a published article that describes a similar simulation and adapt their method suitably. Otherwise describe your method more thoroughly (e.g. how large was the box, what ensemble did you use, equilibration regime, etc.) and maybe someone has some judgement they can share with you. Mark From zzhwise1 at 163.com Mon Sep 18 08:01:42 2006 From: zzhwise1 at 163.com (zzhwise1) Date: Mon, 18 Sep 2006 14:01:42 +0800 (CST) Subject: [gmx-users] bond lost (II) Message-ID: <450E3646.000061.12817@bj163app47.163.com> about the second question,is that ,when i use the md as integrator,the feedback show the atomnumber of gro was not the same as top which show 0 atom? but when i use the l-bfgs as integrator, there was no wrong,and goes smoothly! and i never know why! -------------- next part -------------- An HTML attachment was scrubbed... URL: From Mark.Abraham at anu.edu.au Mon Sep 18 08:22:09 2006 From: Mark.Abraham at anu.edu.au (Mark Abraham) Date: Mon, 18 Sep 2006 16:22:09 +1000 Subject: [gmx-users] bond lost (II) In-Reply-To: <450E3646.000061.12817@bj163app47.163.com> References: <450E3646.000061.12817@bj163app47.163.com> Message-ID: <450E3B11.1020501@anu.edu.au> zzhwise1 wrote: > about the second question,is that ,when i use the md as integrator,the > feedback show the atomnumber of gro was not the same as top which show 0 > atom? but when i use the l-bfgs as integrator, there was no wrong,and > goes smoothly! > and i never know why! Neither will we know, unless you can do as I suggested last time - "You need to describe the problem fully, include contents of small files where appropriate, and quote the feedback you get from the gromacs tools." Mark From jiqing at iccas.ac.cn Mon Sep 18 08:51:37 2006 From: jiqing at iccas.ac.cn (=?gb2312?B?1vfUwiCjuqOp?=) Date: Mon, 18 Sep 2006 14:51:37 +0800 Subject: [gmx-users] The molecule size Message-ID: <000a01c6daee$e3600430$851ae29f@jiqing> > Hi: > > Two melt models were built for polyethylene (PE) and > polyvinylmethylether (PVME) melt with PBC condition . > > The density of both melt model agree with experimenal value well.But > when one check the radius of gyration (Rg) of them, both of them were > too small to accept as follows. > > The Rg for PE (C1000) is just 28 angstrom. It means the infinite > charaterastic ratio (Cinf) for the polymer is just about 2 which is much > smaller than scatter experimental value about 7. > > The Rg for PVME (C44) melt is about 6.6 angstrom. It means the Cinf for > the polymer is just 2.5 which is much smaller than scatter experimental > value 8-10. > > Can these results be accepted? > > Is there any fault in force field? gromos96a Usually a garbage result as output means that you had either garbage as input, or garbage for the algorithm. Find a published article that describes a similar simulation and adapt their method suitably. Otherwise describe your method more thoroughly (e.g. how large was the box, what ensemble did you use, equilibration regime, etc.) and maybe someone has some judgement they can share with you. Mark Hi Mark: Thanks for your advise. Because the PE model is built by one of my officemate, i did not konw its details. The cell length about my PVME model is 4.5 nm which is big enough for a PVME chain possesses all trans conformation. The ensemble is NVT with the control file Pcoupl = no after 10ns NPT simulation to reach the experimental density. The runtime for NVT is 5ns from which the relax time for end to end vector is anaylzed. The relax time is about 1ns. So i think the system has been relaxed enough. Is there any error in my process? Maybe the residue parameter for PVME is also needed for discuss. They are: [ VME ] [ atoms ] ; atom type charge cgnr CN Gasteiger CAB CH1 0.142 1 ; CN CAA CH2 0.035 1 ; CN OAD OE -0.352 1 ; CN CAC CH3 0.174 1 ; CN [ bonds ] ; ai aj fu CAA CAB gb_27 CAB OAD gb_53 CAC OAD gb_53 CAB +CAA gb_27 [ angles ] ; ai aj ak fu c0, c1, ... CAA CAB OAD ga_30 CAB OAD CAC ga_10 OAD CAB +CAA ga_30 CAA CAB +CAA ga_15 CAB +CAA +CAB ga_15 [ dihedrals ] ; ai aj ak al fu c0, c1, m, ... CAA CAB OAD CAC gd_13 CAA CAB +CAA +CAB gd_34 +CAA CAB OAD CAC gd_13 CAB +CAA +CAB +OAD gd_1 ************************************************* Ji Qing Institute of Chemistry, Chinese Academy of Sciences Tel: 0086-10-62562894 ?82618423 ************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From zhaoxiitc2002 at yahoo.com.cn Mon Sep 18 09:12:43 2006 From: zhaoxiitc2002 at yahoo.com.cn (xi zhao) Date: Mon, 18 Sep 2006 15:12:43 +0800 (CST) Subject: [gmx-users] r.m.s.i.p Message-ID: <20060918071243.1399.qmail@web15613.mail.cnb.yahoo.com> Dear Gromacs users: I am a new gromacs user, I want ro calculate r.m.s.i.p for exploring similar in motions of two different proteins, I need a script or tools to calculate it. I need your help! Thank you in advance! Best regard! ___________________________________________________________ Mp3???-??????? http://music.yahoo.com.cn/?source=mail_mailbox_footer From Mark.Abraham at anu.edu.au Mon Sep 18 09:25:31 2006 From: Mark.Abraham at anu.edu.au (Mark Abraham) Date: Mon, 18 Sep 2006 17:25:31 +1000 Subject: [gmx-users] r.m.s.i.p In-Reply-To: <20060918071243.1399.qmail@web15613.mail.cnb.yahoo.com> References: <20060918071243.1399.qmail@web15613.mail.cnb.yahoo.com> Message-ID: <450E49EB.2010808@anu.edu.au> xi zhao wrote: > Dear Gromacs users: > I am a new gromacs user, I want ro calculate r.m.s.i.p > for exploring similar in motions of two different > proteins, I need a script or tools to calculate it. I > need your help! I don't know what r.m.s.i.p is. If you want to get help, please define carefully what you are trying to do - even a link to a journal article might work. Please read carefully the gromacs manual section that describes what the utility programs do, in case one of them does it. Mark From zhaoxiitc2002 at yahoo.com.cn Mon Sep 18 09:48:28 2006 From: zhaoxiitc2002 at yahoo.com.cn (xi zhao) Date: Mon, 18 Sep 2006 15:48:28 +0800 (CST) Subject: =?gb2312?q?=BB=D8=B8=B4=A3=BA=20Re:=20[gmx-users]=20r.m.s.i.p?= In-Reply-To: <450E49EB.2010808@anu.edu.au> Message-ID: <20060918074828.23261.qmail@web15601.mail.cnb.yahoo.com> Based on the essential dynamics analysis, the similar of the internal fluctuations in may simulation systems was evaluated by comparing principal subspace first 10 eigenvectors) of each structural trajectory by using the root mean square inner product(RMSIP). Amadei, A., de groot, B. L., Ceruso, M. A., Paci, M., Di Nola, A. & Berendsen, H. J. A kinetic model for the internal motions of proteins: diffusion between multiple harmonic wells. Proteins. 1999. 35, 283-292. Mark Abraham ??? xi zhao wrote: > Dear Gromacs users: > I am a new gromacs user, I want ro calculate r.m.s.i.p > for exploring similar in motions of two different > proteins, I need a script or tools to calculate it. I > need your help! I don't know what r.m.s.i.p is. If you want to get help, please define carefully what you are trying to do - even a link to a journal article might work. Please read carefully the gromacs manual section that describes what the utility programs do, in case one of them does it. Mark _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php --------------------------------- Mp3???-??????? -------------- next part -------------- An HTML attachment was scrubbed... URL: From zgxjlx at gmail.com Mon Sep 18 10:03:59 2006 From: zgxjlx at gmail.com (liu xin) Date: Mon, 18 Sep 2006 16:03:59 +0800 Subject: [gmx-users] Re: Simulation problem with extended membrane system! In-Reply-To: <1158120208.4507831024ac2@webmail.utoronto.ca> References: <1158120208.4507831024ac2@webmail.utoronto.ca> Message-ID: Thanks Chris, I really appreciate your help! I've got my extended membrane system regarding your note, and now I'm testing it with my GPCR. I am still not very familiar with the script, I think it will take some time to learn. Thanks again! On 9/13/06, chris.neale at utoronto.ca wrote: > > >If I solvate my GPCR into the DPPC128 system using genbox, there are only > >about 50 lipids left, which I think are too few, so I want a larger > starting > >structure. > > >According to your note, when I did step 3, loaded my DPPC183 system to > VMD, > >I found the edges lined up poorly, there is are gaps between two periodic > >cells. I also try other system like DPPC200, DPPC150, but only the > original > >dppc128 system, I've equilibrated it for 2ns, have no gap between two > >periodic cells. > > >So, I will try another starting structure, like POPC, DMPC or your POPE. > But > >I still can't figure out why there are gaps when using genbox to extend > the > >DPPC system. > > It's because any overlap causes an entire lipid to be removed. > If you don't want to equilibrate, try exactly doubling your system size in > x and > y. That should work perfectly. > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zhaoxiitc2002 at yahoo.com.cn Mon Sep 18 10:15:43 2006 From: zhaoxiitc2002 at yahoo.com.cn (xi zhao) Date: Mon, 18 Sep 2006 16:15:43 +0800 (CST) Subject: =?gb2312?q?=BB=D8=B8=B4=A3=BA=20Re:=20[gmx-users]=20r.m.s.i.p?= In-Reply-To: <450E49EB.2010808@anu.edu.au> Message-ID: <20060918081543.25030.qmail@web15613.mail.cnb.yahoo.com> Based on the essential dynamics analysis, the similar of the internal fluctuations in may simulation systems was evaluated by comparing principal subspace first 10 eigenvectors) of each structural trajectory by using the root mean square inner product(RMSIP). Amadei, A., de groot, B. L., Ceruso, M. A., Paci, M., Di Nola, A. & Berendsen, H. J. A kinetic model for the internal motions of proteins: diffusion between multiple harmonic wells. Proteins. 1999. 35, 283-292. Mark Abraham ??? xi zhao wrote: > Dear Gromacs users: > I am a new gromacs user, I want ro calculate r.m.s.i.p > for exploring similar in motions of two different > proteins, I need a script or tools to calculate it. I > need your help! I don't know what r.m.s.i.p is. If you want to get help, please define carefully what you are trying to do - even a link to a journal article might work. Please read carefully the gromacs manual section that describes what the utility programs do, in case one of them does it. Mark _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php --------------------------------- ??????-3.5G???20M?? -------------- next part -------------- An HTML attachment was scrubbed... URL: From tsjerkw at gmail.com Mon Sep 18 10:56:26 2006 From: tsjerkw at gmail.com (Tsjerk Wassenaar) Date: Mon, 18 Sep 2006 10:56:26 +0200 Subject: =?GB2312?B?UmU6ILvYuLSjuiBSZTogW2dteC11c2Vyc10gci5tLnMuaS5w?= In-Reply-To: <20060918081543.25030.qmail@web15613.mail.cnb.yahoo.com> References: <450E49EB.2010808@anu.edu.au> <20060918081543.25030.qmail@web15613.mail.cnb.yahoo.com> Message-ID: <8ff898150609180156xf26c9eel1caf18ef940b5da9@mail.gmail.com> Hi Xi Zhao, Please find attached a .csh script you can use to calculate the rmsip. The script is of the hand of Isabella Daidone, now in Heidelberg. Note that for a set of 'equal' simulations there is a spread in the values you obtain for the RMSIP (i.e. it's not an absolute measure of equality unless you have full convergence of your simulations). If you want to use the RMSIP to really compare simulations check our paper in JCC 27 p. 316 (2006). Cheers, Tsjerk On 9/18/06, xi zhao wrote: > Based on the essential dynamics analysis, the similar of the internal > fluctuations in may simulation systems was evaluated by comparing principal > subspace first 10 eigenvectors) of each structural trajectory by using the > root mean square inner product(RMSIP). > Amadei, A., de groot, B. L., Ceruso, M. A., Paci, M., Di Nola, A. & > Berendsen, H. J. A kinetic model for the internal motions of proteins: > diffusion between multiple harmonic wells. Proteins. 1999. 35, 283-292. > > Mark Abraham ??? > xi zhao wrote: > > Dear Gromacs users: > > I am a new gromacs user, I want ro calculate r.m.s.i.p > > for exploring similar in motions of two different > > proteins, I need a script or tools to calculate it. I > > need your help! > > I don't know what r.m.s.i.p is. If you want to get help, please define > carefully what you are trying to do - even a link to a journal article > might work. Please read carefully the gromacs manual section that > describes what the utility programs do, in case one of them does it. > > Mark > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > > > ________________________________ > ??????-3.5G???20M?? > > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > -- Tsjerk A. Wassenaar, Ph.D. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 -------------- next part -------------- A non-text attachment was scrubbed... Name: xpm2normal.csh Type: application/x-csh Size: 2063 bytes Desc: not available URL: From raja_28 at fastmail.us Mon Sep 18 10:26:44 2006 From: raja_28 at fastmail.us (raja) Date: Mon, 18 Sep 2006 01:26:44 -0700 Subject: 回复： Re: [gmx-users] r.m.s.i.p In-Reply-To: <20060918081543.25030.qmail@web15613.mail.cnb.yahoo.com> References: <20060918081543.25030.qmail@web15613.mail.cnb.yahoo.com> Message-ID: <1158568004.17349.271172101@webmail.messagingengine.com> HI Zhao, To compute RMSIP, you have to compute eigenvector using gromacs utility program then from that trajectory you can compute RMSIP using a script which I got from Tsjerk Wassenaar from this list. You can appraoch him. Regards, B.Nataraj On Mon, 18 Sep 2006 16:15:43 +0800 (CST), "xi zhao" said: > Based on the essential dynamics analysis, the similar of the internal > fluctuations in may simulation systems was evaluated by comparing > principal subspace first 10 eigenvectors) of each structural trajectory > by using the root mean square inner product(RMSIP). Amadei, A., > de groot, B. L., Ceruso, M. A., Paci, M., Di Nola, A. & Berendsen, H. J. > A kinetic model for the internal motions of proteins: diffusion between > multiple harmonic wells. Proteins. 1999. 35, 283-292. > > > Mark Abraham 写道： xi zhao wrote: > > Dear Gromacs users: > > I am a new gromacs user, I want ro calculate r.m.s.i.p > > for exploring similar in motions of two different > > proteins, I need a script or tools to calculate it. I > > need your help! > > I don't know what r.m.s.i.p is. If you want to get help, please define > carefully what you are trying to do - even a link to a journal article > might work. Please read carefully the gromacs manual section that > describes what the utility programs do, in case one of them does it. > > Mark > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > --------------------------------- > 雅虎免费邮箱-3.5G容量，20M附件 -- raja raja_28 at fastmail.us -- http://www.fastmail.fm - I mean, what is it about a decent email service? From asillanp at csc.fi Mon Sep 18 12:53:25 2006 From: asillanp at csc.fi (=?ISO-8859-1?Q?Atte_Sillanp=E4=E4?=) Date: Mon, 18 Sep 2006 13:53:25 +0300 (EEST) Subject: [gmx-users] short range nonbondeds = 0 in power4 In-Reply-To: References: <45096485.3080603@xray.bmc.uu.se> <4509B7CD.5050802@xray.bmc.uu.se> Message-ID: On Fri, 15 Sep 2006, Atte Sillanp?? wrote: >>>>> I've run into a mysterious problem. The versions 3.3. and 3.3.1 compile >>>>> and execute, but the short range coulomb and LJ energies come out as >>>>> zero when using the mpi-version. Serial code works ok (mpi version gives >>>>> zero if run using just one cpu). No errors, no warnings. Hi, the problem seems solved. I removed the --enable-threads from the gromacs config options and now short range forces come out right. Simulations are stable and e.g. water rdfs are identical in power4 and amd opteron. It's a little bit nasty that compiler gets through the threads flag but then computes garbage. It has been said in the mailing list that threads don't work yet, but that's hard to find as the solution unless you know to look for it. To further check my binary I'd like to do some other tests. I tried looking for the benchmarks, but the link doesn't work (search for 'bench' at the gromacs site). Are they still available (and do they have some verified results to compare to?) Thanks, Atte From spoel at xray.bmc.uu.se Mon Sep 18 14:38:14 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Mon, 18 Sep 2006 07:38:14 -0500 Subject: [gmx-users] short range nonbondeds = 0 in power4 In-Reply-To: References: <45096485.3080603@xray.bmc.uu.se> <4509B7CD.5050802@xray.bmc.uu.se> Message-ID: <450E9336.6050300@xray.bmc.uu.se> Atte Sillanp?? wrote: > On Fri, 15 Sep 2006, Atte Sillanp?? wrote: > >>>>>> I've run into a mysterious problem. The versions 3.3. and 3.3.1 >>>>>> compile >>>>>> and execute, but the short range coulomb and LJ energies come out as >>>>>> zero when using the mpi-version. Serial code works ok (mpi version >>>>>> gives >>>>>> zero if run using just one cpu). No errors, no warnings. > > Hi, > > the problem seems solved. I removed the --enable-threads from the > gromacs config options and now short range forces come out right. > Simulations are stable and e.g. water rdfs are identical in power4 and > amd opteron. It's a little bit nasty that compiler gets through the > threads flag but then computes garbage. > > It has been said in the mailing list that threads don't work yet, but > that's hard to find as the solution unless you know to look for it. > > To further check my binary I'd like to do some other tests. I tried > looking for the benchmarks, but the link doesn't work (search for > 'bench' at the gromacs site). Are they still available (and do they > have some verified results to compare to?) > > Thanks, For now you can download them using good old ftp (user anonymous pass your email) We will fix the website. > > Atte > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From spoel at xray.bmc.uu.se Mon Sep 18 14:45:17 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Mon, 18 Sep 2006 07:45:17 -0500 Subject: [gmx-users] The molecule size In-Reply-To: <000a01c6daee$e3600430$851ae29f@jiqing> References: <000a01c6daee$e3600430$851ae29f@jiqing> Message-ID: <450E94DD.5060204@xray.bmc.uu.se> ?? ?? wrote: > > Hi: > > > > Two melt models were built for polyethylene (PE) and > > polyvinylmethylether (PVME) melt with PBC condition . > > > > The density of both melt model agree with experimenal value well.But > > when one check the radius of gyration (Rg) of them, both of them were > > too small to accept as follows. > > > > The Rg for PE (C1000) is just 28 angstrom. It means the infinite > > charaterastic ratio (Cinf) for the polymer is just about 2 which is much > > smaller than scatter experimental value about 7. > > > > The Rg for PVME (C44) melt is about 6.6 angstrom. It means the Cinf for > > the polymer is just 2.5 which is much smaller than scatter experimental > > value 8-10. > > > > Can these results be accepted? > > > > Is there any fault in force field? gromos96a Two things, - maybe you need a larger systems - maybe g_gyrate does not take periodicity into account correctly. extract some single molecules and look at them in a viewer, or write your own script to compute Rg. - have you used pbc = full for the simulations? > > Usually a garbage result as output means that you had either garbage as > input, or garbage for the algorithm. Find a published article that > describes a similar simulation and adapt their method suitably. > Otherwise describe your method more thoroughly (e.g. how large was the > box, what ensemble did you use, equilibration regime, etc.) and maybe > someone has some judgement they can share with you. > > Mark > > *Hi Mark:* > *Thanks for your advise. Because the PE model is built by one of my > officemate, i did not konw its details.* > ** > *The cell length about my PVME model is 4.5 nm which is big enough for a > PVME chain possesses all trans conformation. The ensemble is NVT with > the control file Pcoupl = no after 10ns NPT simulation to reach the > experimental density. The runtime for NVT is 5ns from which the relax > time for end to end vector is anaylzed. The relax time is about 1ns. So > i think the system has been relaxed enough.* > ** > *Is there any error in my process?* > ** > *Maybe the residue parameter for PVME is also needed for discuss. They are:* > ** -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From jaepark at uiuc.edu Mon Sep 18 16:42:37 2006 From: jaepark at uiuc.edu (Jae Hyun Park) Date: Mon, 18 Sep 2006 09:42:37 -0500 (CDT) Subject: [gmx-users] n-hexadecane simulation Message-ID: <20060918094237.ABZ80910@expms1.cites.uiuc.edu> Dear all GROMACS users: I'm simulating n-hexadecane bulk at 300 K using UA model with fixed bond length, harmonic angle potential, and Rychaert-Bellemans torsion model. However, it is so unstable for 2fs time step - The bond length suddenly diverges. The simulation becomes stable for 0.2 fs time step, which seems too small. Could anybody give an instruction for this problem? Followings are my .mdp and topology files. Thank you in advance for your kind instruction. ; VARIOUS PREPROCESSING OPTIONS = title = 2*2 pore cpp = /lib/cpp integrator = md dt = 0.002 nsteps = 6000000 nstcomm = 1 nstxout = 1000 nstvout = 1000 nstfout = 1000 nstlog = 1000 nstenergy = 1000 ;Output frequency and precision for xtc file = nstxtcout = 500 xtc_precision = 10000 xtc-grps = HEX ; CONSTRAINT SCHEME constraints = all-bonds constraint_algorithm = lincs ; Selection of energy groups = energygrps = HEX ; NEIGHBORSEARCHING PARAMETERS = nstlist = 10 ns_type = grid pbc = xyz ; OPTIONS FOR WEAK COUPLING ALGORITHMS = tcoupl = nose-hoover tc-grps = HEX tau_t = 0.3 ref_t = 300.0 rcoulomb = 1.49 rlist = 1.38 rvdw = 1.38 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = yes gen_temp = 300.0 gen_seed = 94729 [ moleculetype ] ; molname nrexcl HEX 3 [ atoms ] ; nr type resnr residue atom cgnr charge 1 CH3 1 HEX C1 1 0.000 2 CH2 1 HEX C2 1 0.000 3 CH2 1 HEX C3 1 0.000 4 CH2 1 HEX C4 1 0.000 5 CH2 1 HEX C5 1 0.000 6 CH2 1 HEX C6 1 0.000 7 CH2 1 HEX C7 1 0.000 8 CH2 1 HEX C8 1 0.000 9 CH2 1 HEX C9 1 0.000 10 CH2 1 HEX C10 1 0.000 11 CH2 1 HEX C11 1 0.000 12 CH2 1 HEX C12 1 0.000 13 CH2 1 HEX C13 1 0.000 14 CH2 1 HEX C14 1 0.000 15 CH2 1 HEX C15 1 0.000 16 CH3 1 HEX C16 1 0.000 [ constraints ] 1 2 2 0.153 2 3 2 0.153 3 4 2 0.153 4 5 2 0.153 5 6 2 0.153 6 7 2 0.153 7 8 2 0.153 8 9 2 0.153 9 10 2 0.153 10 11 2 0.153 11 12 2 0.153 12 13 2 0.153 13 14 2 0.153 14 15 2 0.153 15 16 2 0.153 [ angles ] 1 2 3 1 114.0 519.6875 2 3 4 1 114.0 519.6875 3 4 5 1 114.0 519.6875 4 5 6 1 114.0 519.6875 5 6 7 1 114.0 519.6875 6 7 8 1 114.0 519.6875 7 8 9 1 114.0 519.6875 8 9 10 1 114.0 519.6875 9 10 11 1 114.0 519.6875 10 11 12 1 114.0 519.6875 11 12 13 1 114.0 519.6875 12 13 14 1 114.0 519.6875 13 14 15 1 114.0 519.6875 14 15 16 1 114.0 519.6875 [ dihedrals ] 1 2 3 4 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0 2 3 4 5 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0 3 4 5 6 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0 4 5 6 7 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0 5 6 7 8 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0 6 7 8 9 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0 7 8 9 10 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0 8 9 10 11 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0 9 10 11 12 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0 10 11 12 13 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0 11 12 13 14 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0 12 13 14 15 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0 13 14 15 16 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0 ======================================= Jae Hyun Park, Ph.D. Postdoctoral Associate 3221 Beckamn Institute University of Illinois at Urbana-Champaign 405 North Mathews Avenue Urbana, IL 61801 (Tel) 217-244-4353, (FAX) 217-244-4333 (E-mail) jaepark at uiuc.edu From chris.neale at utoronto.ca Mon Sep 18 17:03:14 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Mon, 18 Sep 2006 11:03:14 -0400 Subject: [gmx-users] Re: Simulation problem with extended membrane system! Message-ID: <20060918110314.563p1e8rootso0k4@webmail.utoronto.ca> If you use the script as I have suggested, http://www.gromacs.org/pipermail/gmx-users/2006-May/021526.html The script is designed for a gro file that does not have any velocities written into it, ie. it looks like this: 1THR N 1 0.801 6.473 -0.310 1THR H1 2 0.760 6.476 -0.402 1THR H2 3 0.865 6.394 -0.304 If you have 3 additional columns in your .gro file, then you need to change the script like this: l=${#line} m=$(expr $l - 24) # ADD THIS LINE ONLY IF VELOCITIES ARE IN YOUR .GRO The first line is #37 I think, and the next line is the line that you need to add. This says "Ignore the velocities" Also, if you use TIP4p then line 30 needs to be if [ "$count" = 4 ]; then instead of if [ "$count" = 3 ]; then Likewise, use "5" if you use tip5p. Chris. From frederic.leroy at urv.net Mon Sep 18 17:00:17 2006 From: frederic.leroy at urv.net (Frederic Leroy) Date: Mon, 18 Sep 2006 17:00:17 +0200 Subject: [gmx-users] n-hexadecane simulation In-Reply-To: <20060918094237.ABZ80910@expms1.cites.uiuc.edu> References: <20060918094237.ABZ80910@expms1.cites.uiuc.edu> Message-ID: <450EB481.7010007@urv.net> You could change the lincs_iter. I would use SHAKE rather than LINCS. For n-alkanes using the model of Ryckaert-Bellemans, it is OK. Anyway, 2fs is correct. Jae Hyun Park wrote: >Dear all GROMACS users: > >I'm simulating n-hexadecane bulk at 300 K using UA model with fixed bond length, harmonic angle potential, and Rychaert-Bellemans torsion model. However, it is so unstable for 2fs time step - The bond length suddenly diverges. The simulation becomes stable for 0.2 fs time step, which seems too small. Could anybody give an instruction for this problem? Followings are my .mdp and topology files. > >Thank you in advance for your kind instruction. > > >; VARIOUS PREPROCESSING OPTIONS = >title = 2*2 pore >cpp = /lib/cpp > >integrator = md >dt = 0.002 >nsteps = 6000000 >nstcomm = 1 > >nstxout = 1000 >nstvout = 1000 >nstfout = 1000 >nstlog = 1000 >nstenergy = 1000 > >;Output frequency and precision for xtc file = >nstxtcout = 500 >xtc_precision = 10000 >xtc-grps = HEX > >; CONSTRAINT SCHEME >constraints = all-bonds >constraint_algorithm = lincs > >; Selection of energy groups = >energygrps = HEX > >; NEIGHBORSEARCHING PARAMETERS = >nstlist = 10 >ns_type = grid >pbc = xyz > >; OPTIONS FOR WEAK COUPLING ALGORITHMS = >tcoupl = nose-hoover >tc-grps = HEX >tau_t = 0.3 >ref_t = 300.0 > >rcoulomb = 1.49 >rlist = 1.38 >rvdw = 1.38 > > ; GENERATE VELOCITIES FOR STARTUP RUN = >gen_vel = yes >gen_temp = 300.0 >gen_seed = 94729 > >[ moleculetype ] >; molname nrexcl >HEX 3 > >[ atoms ] >; nr type resnr residue atom cgnr charge > 1 CH3 1 HEX C1 1 0.000 > 2 CH2 1 HEX C2 1 0.000 > 3 CH2 1 HEX C3 1 0.000 > 4 CH2 1 HEX C4 1 0.000 > 5 CH2 1 HEX C5 1 0.000 > 6 CH2 1 HEX C6 1 0.000 > 7 CH2 1 HEX C7 1 0.000 > 8 CH2 1 HEX C8 1 0.000 > 9 CH2 1 HEX C9 1 0.000 > 10 CH2 1 HEX C10 1 0.000 > 11 CH2 1 HEX C11 1 0.000 > 12 CH2 1 HEX C12 1 0.000 > 13 CH2 1 HEX C13 1 0.000 > 14 CH2 1 HEX C14 1 0.000 > 15 CH2 1 HEX C15 1 0.000 > 16 CH3 1 HEX C16 1 0.000 > >[ constraints ] > 1 2 2 0.153 > 2 3 2 0.153 > 3 4 2 0.153 > 4 5 2 0.153 > 5 6 2 0.153 > 6 7 2 0.153 > 7 8 2 0.153 > 8 9 2 0.153 > 9 10 2 0.153 > 10 11 2 0.153 > 11 12 2 0.153 > 12 13 2 0.153 > 13 14 2 0.153 > 14 15 2 0.153 > 15 16 2 0.153 > >[ angles ] > 1 2 3 1 114.0 519.6875 > 2 3 4 1 114.0 519.6875 > 3 4 5 1 114.0 519.6875 > 4 5 6 1 114.0 519.6875 > 5 6 7 1 114.0 519.6875 > 6 7 8 1 114.0 519.6875 > 7 8 9 1 114.0 519.6875 > 8 9 10 1 114.0 519.6875 > 9 10 11 1 114.0 519.6875 > 10 11 12 1 114.0 519.6875 > 11 12 13 1 114.0 519.6875 > 12 13 14 1 114.0 519.6875 > 13 14 15 1 114.0 519.6875 > 14 15 16 1 114.0 519.6875 > >[ dihedrals ] > 1 2 3 4 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0 > 2 3 4 5 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0 > 3 4 5 6 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0 > 4 5 6 7 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0 > 5 6 7 8 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0 > 6 7 8 9 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0 > 7 8 9 10 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0 > 8 9 10 11 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0 > 9 10 11 12 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0 > 10 11 12 13 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0 > 11 12 13 14 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0 > 12 13 14 15 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0 > 13 14 15 16 3 4.1987 8.3936 0.5670 -13.1593 0.0 0.0 >======================================= >Jae Hyun Park, Ph.D. >Postdoctoral Associate >3221 Beckamn Institute >University of Illinois at Urbana-Champaign >405 North Mathews Avenue >Urbana, IL 61801 >(Tel) 217-244-4353, (FAX) 217-244-4333 >(E-mail) jaepark at uiuc.edu >_______________________________________________ >gmx-users mailing list gmx-users at gromacs.org >http://www.gromacs.org/mailman/listinfo/gmx-users >Please don't post (un)subscribe requests to the list. Use the >www interface or send it to gmx-users-request at gromacs.org. >Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > From chris.neale at utoronto.ca Mon Sep 18 17:13:03 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Mon, 18 Sep 2006 11:13:03 -0400 Subject: [gmx-users] re: n-hexadecane simulation Message-ID: <20060918111303.563ux0hbxehw8ok8@webmail.utoronto.ca> You have #2 in the 3rd column which nmeans that you are not excluding 1-2, 1-3, or 1-4 Nonbonded interactions as you are intended to. Change this value to a one instead of a two. That should fix your problem. However, I would recommend that you set up the regular RB bonds like this. That way you have the settings in case you want to stop constraining bond lengths. Remove your [ constraints ] section and adding this: [ bonds ] 1 2 1 0.15300E+00 0.33470E+06 2 3 1 0.15300E+00 0.33470E+06 3 4 1 0.15300E+00 0.33470E+06 4 5 1 0.15300E+00 0.33470E+06 5 6 1 0.15300E+00 0.33470E+06 6 7 1 0.15300E+00 0.33470E+06 7 8 1 0.15300E+00 0.33470E+06 8 9 1 0.15300E+00 0.33470E+06 9 10 1 0.15300E+00 0.33470E+06 10 11 1 0.15300E+00 0.33470E+06 11 12 1 0.15300E+00 0.33470E+06 12 13 1 0.15300E+00 0.33470E+06 13 14 1 0.15300E+00 0.33470E+06 14 15 1 0.15300E+00 0.33470E+06 15 16 1 0.15300E+00 0.33470E+06 Chris. From silvasantosster at gmail.com Mon Sep 18 17:26:03 2006 From: silvasantosster at gmail.com (Elias santos) Date: Mon, 18 Sep 2006 12:26:03 -0300 Subject: [gmx-users] Bonds Message-ID: <97baf6380609180826h36f4c713k31b11c64f806da75@mail.gmail.com> Hi! I have a question . I am working with a proteina that they will count two centers FES co-ordinated for cisteins, these cisteins were not on to iron atoms, thus I modified the archive itp only with respect the bonds, no angles or diedrals, to bind to these two residuos. After the minimiza??o, I made one md with restricted position, when I make the total dynamic with I tie occurs error in the algorithm shake and it stops in the first steps informing that I did not obtain to set molecules of water. I am using the field of force of gromacs (option 4) and the water is spc216. ESS -------------- next part -------------- An HTML attachment was scrubbed... URL: From asaxena17 at yahoo.com Mon Sep 18 17:21:46 2006 From: asaxena17 at yahoo.com (Akansha Saxena) Date: Mon, 18 Sep 2006 08:21:46 -0700 (PDT) Subject: [gmx-users] protein unstable for parallel job while stable for serial one Message-ID: <20060918152147.38989.qmail@web60811.mail.yahoo.com> Hello Has anybody seen a protein becoming unstable on parallel nodes while remaining stable on single node? I am running a NPT molecular dynamics simulation. The system contains a protein with 141 residues surrounded by water making the total to 32714 atoms. I ran this simulation at two places for 8ns. One as a serial job and the other as a parallel job on 16 nodes. The protein remains stable all through for the serial job but for parallel job the protein opens up after 3ns of simulation and is never stable after that. All other conditions are exactly the same. Any help would be highly appreciated. Akansha Akansha Saxena Graduate Student Department of Biomedical Engineering Washington University in St Louis __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From fefan at utmb.edu Mon Sep 18 17:25:53 2006 From: fefan at utmb.edu (Fan, Fenghui ) Date: Mon, 18 Sep 2006 10:25:53 -0500 Subject: [gmx-users] merger ligand and protein to constriant References: <358062857.10180@pumc.edu.cn> Message-ID: Try the following way: But you shoul get you top file and gro file without the ligand. Then If your protein has 100 residues, add you ligand as residue 101 in the gro file. After residue add the "TER" . In ddition, adding the ligand ITP file to the later part of the Gro file. -----Original Message----- From: gmx-users-bounces at gromacs.org on behalf of ?? Sent: Tue 9/12/2006 7:07 AM To: gmx-users at gromacs.org Subject: Re:[gmx-users] merger ligand and protein to constriant What about merging the ligand the the protein by DeepView? In your mail: >From: "kanin wichapong" >Reply-To: Discussion list for GROMACS users >To: gmx-users at gromacs.org >Subject: [gmx-users] merger ligand and protein to constriant >Date:Tue, 12 Sep 2006 13:40:59 +0200 > >Hi all > I already look in the turorial however that is not the thing that I try to >look for. I would like to merge the ligand into the protein and then make >the contrain between two atoms, one from the liagand and one from the >protein. However, as far as I know, I can do the constraint or restraint >just in the one chain. I cant do that with the different chain. So that i >try to merge ligand chain and protein chain. I tried to do that with pdb2gmx >but it is not work. So that i would like to know is there any way to merge >the ligand chain with the protein chain. > Thanks for all your suggstions > >Best Regard >Kanin >_______________________________________________ >gmx-users mailing list gmx-users at gromacs.org >http://www.gromacs.org/mailman/listinfo/gmx-users >Please don't post (un)subscribe requests to the list. Use the >www interface or send it to gmx-users-request at gromacs.org. >Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php From fefan at utmb.edu Mon Sep 18 17:29:33 2006 From: fefan at utmb.edu (Fan, Fenghui ) Date: Mon, 18 Sep 2006 10:29:33 -0500 Subject: [gmx-users] r.m.s.i.p References: <20060918071243.1399.qmail@web15613.mail.cnb.yahoo.com> Message-ID: Try RMSD fit function. -----Original Message----- From: gmx-users-bounces at gromacs.org on behalf of xi zhao Sent: Mon 9/18/2006 2:12 AM To: gmx-users at gromacs.org Subject: [gmx-users] r.m.s.i.p Dear Gromacs users: I am a new gromacs user, I want ro calculate r.m.s.i.p for exploring similar in motions of two different proteins, I need a script or tools to calculate it. I need your help! Thank you in advance! Best regard! ___________________________________________________________ Mp3???-??????? http://music.yahoo.com.cn/?source=mail_mailbox_footer _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php From jaepark at uiuc.edu Mon Sep 18 19:10:50 2006 From: jaepark at uiuc.edu (Jae Hyun Park) Date: Mon, 18 Sep 2006 12:10:50 -0500 (CDT) Subject: [gmx-users] re: n-hexadecane simulation Message-ID: <20060918121050.ACA03388@expms1.cites.uiuc.edu> Thank you so much for your consideration. However, it still diverge even after correcting the number in 3rd column and using bond parameters. Also, using SHAKE is not helpful. I'm using single-precision GROMACS. Is it make this kind of problem? What else can I do try? Thank you in advance for your kind instruction. Jae ---- Original message ---- >Date: Mon, 18 Sep 2006 11:13:03 -0400 >From: chris.neale at utoronto.ca >Subject: [gmx-users] re: n-hexadecane simulation >To: gmx-users at gromacs.org > >You have #2 in the 3rd column which nmeans that you are not excluding >1-2, 1-3, or 1-4 Nonbonded interactions as you are intended to. Change >this value to a one instead of a two. That should fix your problem. >However, I would recommend that you set up the regular RB bonds like >this. That way you have the settings in case you want to stop >constraining bond lengths. > >Remove your [ constraints ] section and adding this: > >[ bonds ] > 1 2 1 0.15300E+00 0.33470E+06 > 2 3 1 0.15300E+00 0.33470E+06 > 3 4 1 0.15300E+00 0.33470E+06 > 4 5 1 0.15300E+00 0.33470E+06 > 5 6 1 0.15300E+00 0.33470E+06 > 6 7 1 0.15300E+00 0.33470E+06 > 7 8 1 0.15300E+00 0.33470E+06 > 8 9 1 0.15300E+00 0.33470E+06 > 9 10 1 0.15300E+00 0.33470E+06 > 10 11 1 0.15300E+00 0.33470E+06 > 11 12 1 0.15300E+00 0.33470E+06 > 12 13 1 0.15300E+00 0.33470E+06 > 13 14 1 0.15300E+00 0.33470E+06 > 14 15 1 0.15300E+00 0.33470E+06 > 15 16 1 0.15300E+00 0.33470E+06 > > >Chris. > >_______________________________________________ >gmx-users mailing list gmx-users at gromacs.org >http://www.gromacs.org/mailman/listinfo/gmx-users >Please don't post (un)subscribe requests to the list. Use the >www interface or send it to gmx-users-request at gromacs.org. >Can't post? Read http://www.gromacs.org/mailing_lists/users.php ======================================= Jae Hyun Park, Ph.D. Postdoctoral Associate 3221 Beckamn Institute University of Illinois at Urbana-Champaign 405 North Mathews Avenue Urbana, IL 61801 (Tel) 217-244-4353, (FAX) 217-244-4333 (E-mail) jaepark at uiuc.edu From g0403186 at nus.edu.sg Mon Sep 18 19:16:13 2006 From: g0403186 at nus.edu.sg (Dai Liang) Date: Tue, 19 Sep 2006 01:16:13 +0800 Subject: [gmx-users] a problem about Coul-LR in energy groups output. Coul-LR is always ZERO ! Message-ID: <000e01c6db46$25122e60$401815ac@stu.nus.edu.sg> I want to analyze the energy during a normal simulation. Some strange things happened. In mdp file, I selected DNA, NA+, SOL for energy groups output. When I analyzed edr file by g_energy, I found Coul_LR is always ZERO. I think my parameters have no problem, rlist = 1.0 rcoulomb = 1.0, rvdw = 1.0. Furthermore, when I selected 'System' for energy output, Coul_LR have some reasonable values. When I do MD simulation in other computer, there is NO output for Coul-LR with the SAME parameter file. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chris.neale at utoronto.ca Mon Sep 18 19:53:37 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Mon, 18 Sep 2006 13:53:37 -0400 Subject: [gmx-users] re: n-hexadecane simulation Message-ID: <20060918135337.44wvoscm9c00osoc@webmail.utoronto.ca> 1. Try the [ bonds ] section that I mentioned earlier and remove the [ constraints ] section. 2. Did you do an energy minimization? If so, what total Energy and max force do you acheive? 3. What is the size of your box? Is it >=3.0nm? Is that also larger than 1.49 + max_n-hexadecane_length? It should be both of these, although only the first issue is likely to show up as an energy error. 4. What vdwtype and coulombtype are you using? This might be problematic: rcoulomb = 1.49 rlist = 1.38 rvdw = 1.38 Try this instead: coulombtype = PME rcoulomb = 0.9 fourierspacing = 0.12 pme_order = 4 vdwtype = cut-off rvdw_switch = 0 rvdw = 1.4 rlist = 0.9 From qiaobf at gmail.com Mon Sep 18 22:05:15 2006 From: qiaobf at gmail.com (Qiao Baofu) Date: Mon, 18 Sep 2006 22:05:15 +0200 Subject: [gmx-users] Gromacs install question Message-ID: <6a91f07b0609181305v3b711cdbi501e954720542a29@mail.gmail.com> Hi all, I have a question on installing gromacs: I have installed gromacs 3.3.1 on my computer. And it works. Today, I want to change one commands, so I reinstalled it in the following process: 1. remove the formal direcory of gromacs 2. change to the installation directory of gromacs 3. ./configure 4. make 5 make install The result is that only the following commands are installed in /bin directory of gromacs: ffscan, gmxcheck, gmxdump, grompp,luck, mdrun, pdb2gmx,protonate,tpbconv, x2top. What wrong with it? who can tell me? Thanks in advance! -- Sincerely yours, ********************************************** Baofu Qiao, PhD Frankfurt Institute for Advanced Studies Max-von-Laue-Str. 1 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From reynier at fq.uh.cu Mon Sep 18 21:47:10 2006 From: reynier at fq.uh.cu (=?iso-8859-1?Q?Reynier_Suardiaz_del_R=EDo?=) Date: Mon, 18 Sep 2006 15:47:10 -0400 Subject: [gmx-users] single point calculation Message-ID: <007601c6db5b$3e0b9090$2c03060a@ESPECTRO> Hi, is my firt question in the list, i have a very simple and posibly a very nonsense question. do i have to use mdrun to performe a single point calculation of a certain conformation? how? is there something to specify in .mdp file? Can some body provide me an example of how to use ffscan? with a small molecule if it is possible... Best regards reynier -------------- next part -------------- An HTML attachment was scrubbed... URL: From silvasantosster at gmail.com Mon Sep 18 23:02:26 2006 From: silvasantosster at gmail.com (Elias santos) Date: Mon, 18 Sep 2006 18:02:26 -0300 Subject: [gmx-users] bonds Message-ID: <97baf6380609181402x5e1736c3g2d5ecf186de63b3e@mail.gmail.com> Hi! I have a question . I am working with a protein that they will count two centers FES co-ordinated for cisteins, these cisteins were not on to iron atoms, thus I modified the archive itp only with respect the bonds, no angles or diedrals, to bind to these two residuos. After the minimiza??o, I made one md with restricted position, when I make the total dynamic with I tie occurs error in the algorithm shake and it stops in the first steps informing that I did not obtain to set molecules of water. I am using the field of force of gromacs (option 4) and the water is spc216. ESS -------------- next part -------------- An HTML attachment was scrubbed... URL: From prasad.gajula at uni-osnabrueck.de Mon Sep 18 23:48:19 2006 From: prasad.gajula at uni-osnabrueck.de (Prasad Gajula) Date: Mon, 18 Sep 2006 23:48:19 +0200 (CEST) Subject: [gmx-users] velocities In-Reply-To: <20060918200640.E6D1A2407B@xray.bmc.uu.se> References: <20060918200640.E6D1A2407B@xray.bmc.uu.se> Message-ID: <1067.131.173.252.1.1158616099.squirrel@webmail.rz.uni-osnabrueck.de> Dear Gromacs Users, I am getting different results for simulations with " gen_vel=yes" and "gen_vel= no". I have generated velocities only for PR MD at 300K. after that I set ' gen_vel= no ' in mdp file. After the position restrained MD , I slowly increased the temparature from 80K , 100K , 200K and last 300K. (with 'gen_vel=no' for all MD) Is it correct? Because I read both 'yes' and 'no' as possibilites in some references. Iam bit confused which to use for exact simulations. Any help will be appreciated. Thanks in advance Best regards Gajula From fefan at utmb.edu Tue Sep 19 01:04:43 2006 From: fefan at utmb.edu (Fan, Fenghui ) Date: Mon, 18 Sep 2006 18:04:43 -0500 Subject: [gmx-users] Gromacs install question References: <6a91f07b0609181305v3b711cdbi501e954720542a29@mail.gmail.com> Message-ID: In your sudirectory of the newly established Gromacs directory, there will subdirectory tools and kernel. You can start your commands in these subdirectory and it should work. Best regards. Fenghui Fan -----Original Message----- From: gmx-users-bounces at gromacs.org on behalf of Qiao Baofu Sent: Mon 9/18/2006 3:05 PM To: Discussion list for GROMACS users Subject: [gmx-users] Gromacs install question Hi all, I have a question on installing gromacs: I have installed gromacs 3.3.1 on my computer. And it works. Today, I want to change one commands, so I reinstalled it in the following process: 1. remove the formal direcory of gromacs 2. change to the installation directory of gromacs 3. ./configure 4. make 5 make install The result is that only the following commands are installed in /bin directory of gromacs: ffscan, gmxcheck, gmxdump, grompp,luck, mdrun, pdb2gmx,protonate,tpbconv, x2top. What wrong with it? who can tell me? Thanks in advance! -- Sincerely yours, ********************************************** Baofu Qiao, PhD Frankfurt Institute for Advanced Studies Max-von-Laue-Str. 1 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ********************************************** From zhaoxiitc2002 at yahoo.com.cn Tue Sep 19 02:12:18 2006 From: zhaoxiitc2002 at yahoo.com.cn (xi zhao) Date: Tue, 19 Sep 2006 08:12:18 +0800 (CST) Subject: =?gb2312?q?=BB=D8=B8=B4=A3=BA=20RE:=20[gmx-users]=20r.m.s.i.p?= In-Reply-To: Message-ID: <20060919001218.79990.qmail@web15611.mail.cnb.yahoo.com> how to use it in detail?Thanks! "Fan, Fenghui " ??? Try RMSD fit function. -----Original Message----- From: gmx-users-bounces at gromacs.org on behalf of xi zhao Sent: Mon 9/18/2006 2:12 AM To: gmx-users at gromacs.org Subject: [gmx-users] r.m.s.i.p Dear Gromacs users: I am a new gromacs user, I want ro calculate r.m.s.i.p for exploring similar in motions of two different proteins, I need a script or tools to calculate it. I need your help! Thank you in advance! Best regard! ___________________________________________________________ Mp3???-??????? http://music.yahoo.com.cn/?source=mail_mailbox_footer _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php --------------------------------- ????????-3.5G???20M??? -------------- next part -------------- An HTML attachment was scrubbed... URL: From zhaoxiitc2002 at yahoo.com.cn Tue Sep 19 02:19:13 2006 From: zhaoxiitc2002 at yahoo.com.cn (xi zhao) Date: Tue, 19 Sep 2006 08:19:13 +0800 (CST) Subject: =?gb2312?q?=BB=D8=B8=B4=A3=BA=20Re:=20=BB=D8=B8=B4=A3=BA=20Re:=20[gmx-use?= =?gb2312?q?rs]=20r.m.s.i.p?= In-Reply-To: <8ff898150609180156xf26c9eel1caf18ef940b5da9@mail.gmail.com> Message-ID: <20060919001913.56606.qmail@web15615.mail.cnb.yahoo.com> Dear Tsjerk : Thank you very much! Tsjerk Wassenaar ??? Hi Xi Zhao, Please find attached a .csh script you can use to calculate the rmsip. The script is of the hand of Isabella Daidone, now in Heidelberg. Note that for a set of 'equal' simulations there is a spread in the values you obtain for the RMSIP (i.e. it's not an absolute measure of equality unless you have full convergence of your simulations). If you want to use the RMSIP to really compare simulations check our paper in JCC 27 p. 316 (2006). Cheers, Tsjerk On 9/18/06, xi zhao wrote: > Based on the essential dynamics analysis, the similar of the internal > fluctuations in may simulation systems was evaluated by comparing principal > subspace first 10 eigenvectors) of each structural trajectory by using the > root mean square inner product(RMSIP). > Amadei, A., de groot, B. L., Ceruso, M. A., Paci, M., Di Nola, A. & > Berendsen, H. J. A kinetic model for the internal motions of proteins: > diffusion between multiple harmonic wells. Proteins. 1999. 35, 283-292. > > Mark Abraham ??? > xi zhao wrote: > > Dear Gromacs users: > > I am a new gromacs user, I want ro calculate r.m.s.i.p > > for exploring similar in motions of two different > > proteins, I need a script or tools to calculate it. I > > need your help! > > I don't know what r.m.s.i.p is. If you want to get help, please define > carefully what you are trying to do - even a link to a journal article > might work. Please read carefully the gromacs manual section that > describes what the utility programs do, in case one of them does it. > > Mark > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > > > ________________________________ > ??????-3.5G???20M?? > > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > -- Tsjerk A. Wassenaar, Ph.D. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php --------------------------------- Mp3???-??????? -------------- next part -------------- An HTML attachment was scrubbed... URL: From zhaoxiitc2002 at yahoo.com.cn Tue Sep 19 02:32:02 2006 From: zhaoxiitc2002 at yahoo.com.cn (xi zhao) Date: Tue, 19 Sep 2006 08:32:02 +0800 (CST) Subject: =?gb2312?q?=BB=D8=B8=B4=A3=BA=20Re:=20=BB=D8=B8=B4=A3=BA=20Re:=20[gmx-use?= =?gb2312?q?rs]=20r.m.s.i.p?= In-Reply-To: <1158568004.17349.271172101@webmail.messagingengine.com> Message-ID: <20060919003202.9911.qmail@web15606.mail.cnb.yahoo.com> Thank you for your advise! raja ??? HI Zhao, To compute RMSIP, you have to compute eigenvector using gromacs utility program then from that trajectory you can compute RMSIP using a script which I got from Tsjerk Wassenaar from this list. You can appraoch him. Regards, B.Nataraj On Mon, 18 Sep 2006 16:15:43 +0800 (CST), "xi zhao" said: > Based on the essential dynamics analysis, the similar of the internal > fluctuations in may simulation systems was evaluated by comparing > principal subspace first 10 eigenvectors) of each structural trajectory > by using the root mean square inner product(RMSIP). Amadei, A., > de groot, B. L., Ceruso, M. A., Paci, M., Di Nola, A. & Berendsen, H. J. > A kinetic model for the internal motions of proteins: diffusion between > multiple harmonic wells. Proteins. 1999. 35, 283-292. > > > Mark Abraham ??? xi zhao wrote: > > Dear Gromacs users: > > I am a new gromacs user, I want ro calculate r.m.s.i.p > > for exploring similar in motions of two different > > proteins, I need a script or tools to calculate it. I > > need your help! > > I don't know what r.m.s.i.p is. If you want to get help, please define > carefully what you are trying to do - even a link to a journal article > might work. Please read carefully the gromacs manual section that > describes what the utility programs do, in case one of them does it. > > Mark > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > --------------------------------- > ??????-3.5G???20M?? -- raja raja_28 at fastmail.us -- http://www.fastmail.fm - I mean, what is it about a decent email service? _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php --------------------------------- ????????-3.5G???20M??? -------------- next part -------------- An HTML attachment was scrubbed... URL: From jake at ncsa.uiuc.edu Tue Sep 19 02:58:49 2006 From: jake at ncsa.uiuc.edu (Eric Jakobsson) Date: Mon, 18 Sep 2006 19:58:49 -0500 Subject: [gmx-users] job opportunity Message-ID: <7.0.0.16.2.20060918195529.04406028@ncsa.uiuc.edu> I am writing to call this community's attention to the job opportunity at http://www.nanoconductor.org/jobs/NCN_at_UIUC_Lead_Scientist.pdf which would involve Gromacs expertise in addition to other software relevant to nanoscience. Thanks for your attention, Eric --------------------------------- Eric Jakobsson, Ph.D. Professor, Department of Molecular and Integrative Physiology, and of Biochemistry, and of the Center for Biophysics and Computational Biology Senior Research Scientist, National Center for Supercomputing Applications Professor, Beckman Institute for Advanced Science and Technology 3261 Beckman Institute, mc251 University of Illinois, Urbana, IL 61801 ph. 217-244-2896 fax 217-244-2909 From Mark.Abraham at anu.edu.au Tue Sep 19 03:31:19 2006 From: Mark.Abraham at anu.edu.au (Mark Abraham) Date: Tue, 19 Sep 2006 11:31:19 +1000 Subject: [gmx-users] velocities In-Reply-To: <1067.131.173.252.1.1158616099.squirrel@webmail.rz.uni-osnabrueck.de> References: <20060918200640.E6D1A2407B@xray.bmc.uu.se> <1067.131.173.252.1.1158616099.squirrel@webmail.rz.uni-osnabrueck.de> Message-ID: <450F4867.1070903@anu.edu.au> Prasad Gajula wrote: > Dear Gromacs Users, > > I am getting different results for simulations with " gen_vel=yes" and > "gen_vel= no". This is expected. No two simulations will be the same unless you run then on the same hardware with exactly the same inputs. gen_vel requires the use of a random number seed. What you want to do, is after equilibration, be sampling from the correct ensemble. > I have generated velocities only for PR MD at 300K. after that I set ' > gen_vel= no ' in mdp file. After the position restrained MD , I slowly > increased the temparature from 80K , 100K , 200K and last 300K. (with > 'gen_vel=no' for all MD) > Is it correct? Because I read both 'yes' and 'no' as possibilites in some > references. Iam bit confused which to use for exact simulations. Personally, I don't think the practice of velocity reassignment in incremental heating while using position restraints is demonstrably better than not using reassignment in incremental heating. Mark From Mark.Abraham at anu.edu.au Tue Sep 19 03:44:31 2006 From: Mark.Abraham at anu.edu.au (Mark Abraham) Date: Tue, 19 Sep 2006 11:44:31 +1000 Subject: [gmx-users] Gromacs install question In-Reply-To: <6a91f07b0609181305v3b711cdbi501e954720542a29@mail.gmail.com> References: <6a91f07b0609181305v3b711cdbi501e954720542a29@mail.gmail.com> Message-ID: <450F4B7F.2020102@anu.edu.au> Qiao Baofu wrote: > Hi all, > > I have a question on installing gromacs: > I have installed gromacs 3.3.1 on my computer. And it works. Today, I > want to change one commands, so I reinstalled it in the following process: > 1. remove the formal direcory of gromacs > 2. change to the installation directory of gromacs > 3. ./configure > 4. make > 5 make install > > The result is that only the following commands are installed in /bin > directory of gromacs: ffscan, gmxcheck, gmxdump, grompp,luck, mdrun, > pdb2gmx,protonate,tpbconv, x2top. > > What wrong with it? who can tell me? Thanks in advance! Probably you didn't do those five steps as described :-) Why is this a problem? Just do it again. Mark From Mark.Abraham at anu.edu.au Tue Sep 19 03:50:27 2006 From: Mark.Abraham at anu.edu.au (Mark Abraham) Date: Tue, 19 Sep 2006 11:50:27 +1000 Subject: [gmx-users] single point calculation In-Reply-To: <007601c6db5b$3e0b9090$2c03060a@ESPECTRO> References: <007601c6db5b$3e0b9090$2c03060a@ESPECTRO> Message-ID: <450F4CE3.4070104@anu.edu.au> Reynier Suardiaz del R?o wrote: > > Hi, is my firt question in the list, i have a very simple and posibly a > very nonsense question. > do i have to use mdrun to performe a single point calculation of a > certain conformation? how? is there something to specify in .mdp file? Just do a zero step minimization. > Can some body provide me an example of how to use ffscan? with a small > molecule if it is possible... Not I. By the way, leaping straight into force field modification before acquiring some experince with gromacs (and/or MD in general) seems to me an excessively masochistic thing to want to do. Mark From jiqing at iccas.ac.cn Tue Sep 19 04:01:06 2006 From: jiqing at iccas.ac.cn (=?gb2312?B?1vfUwiCjuqOp?=) Date: Tue, 19 Sep 2006 10:01:06 +0800 Subject: [gmx-users] Re: The molecule size (jiqing) Message-ID: <002101c6db8f$784a0140$851ae29f@jiqing> Hi: > > > > Two melt models were built for polyethylene (PE) and > > polyvinylmethylether (PVME) melt with PBC condition . > > > > The density of both melt model agree with experimenal value well.But > > when one check the radius of gyration (Rg) of them, both of them were > > too small to accept as follows. > > > > The Rg for PE (C1000) is just 28 angstrom. It means the infinite > > charaterastic ratio (Cinf) for the polymer is just about 2 which is much > > smaller than scatter experimental value about 7. > > > > The Rg for PVME (C44) melt is about 6.6 angstrom. It means the Cinf for > > the polymer is just 2.5 which is much smaller than scatter experimental > > value 8-10. > > > > Can these results be accepted? > > > > Is there any fault in force field? gromos96a Two things, - maybe you need a larger systems - maybe g_gyrate does not take periodicity into account correctly. extract some single molecules and look at them in a viewer, or write your own script to compute Rg. - have you used pbc = full for the simulations? 1.The cell length about my PVME model is 4.5 nm which is big enough for a PVME chain possesses all trans conformation. 2. The Rg is anaylzed by my own program, which has been validated. 3.PBC=XYZ > > Usually a garbage result as output means that you had either garbage as > input, or garbage for the algorithm. Find a published article that > describes a similar simulation and adapt their method suitably. > Otherwise describe your method more thoroughly (e.g. how large was the > box, what ensemble did you use, equilibration regime, etc.) and maybe > someone has some judgement they can share with you. > > Mark > > *Hi Mark:* > *Thanks for your advise. Because the PE model is built by one of my > officemate, i did not konw its details.* > ** > *The cell length about my PVME model is 4.5 nm which is big enough for a > PVME chain possesses all trans conformation. The ensemble is NVT with > the control file Pcoupl = no after 10ns NPT simulation to reach the > experimental density. The runtime for NVT is 5ns from which the relax > time for end to end vector is anaylzed. The relax time is about 1ns. So > i think the system has been relaxed enough.* > ** > *Is there any error in my process?* > ** > *Maybe the residue parameter for PVME is also needed for discuss. They are:* > [ VME ] [ atoms ] ; atom type charge cgnr CN Gasteiger CAB CH1 0.142 1 ; CN CAA CH2 0.035 1 ; CN OAD OE -0.352 1 ; CN CAC CH3 0.174 1 ; CN [ bonds ] ; ai aj fu CAA CAB gb_27 CAB OAD gb_53 CAC OAD gb_53 CAB +CAA gb_27 [ angles ] ; ai aj ak fu c0, c1, ... CAA CAB OAD ga_30 CAB OAD CAC ga_10 OAD CAB +CAA ga_30 CAA CAB +CAA ga_15 CAB +CAA +CAB ga_15 [ dihedrals ] ; ai aj ak al fu c0, c1, m, ... CAA CAB OAD CAC gd_13 CAA CAB +CAA +CAB gd_34 +CAA CAB OAD CAC gd_13 CAB +CAA +CAB +OAD gd_1 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Mark.Abraham at anu.edu.au Tue Sep 19 04:10:55 2006 From: Mark.Abraham at anu.edu.au (Mark Abraham) Date: Tue, 19 Sep 2006 12:10:55 +1000 Subject: [gmx-users] Re: The molecule size (jiqing) In-Reply-To: <002101c6db8f$784a0140$851ae29f@jiqing> References: <002101c6db8f$784a0140$851ae29f@jiqing> Message-ID: <450F51AF.1000507@anu.edu.au> ?? ?? wrote: > Hi: > Two things, > > - maybe you need a larger systems > - maybe g_gyrate does not take periodicity into account correctly. > extract some single molecules and look at them in a viewer, or write > your own script to compute Rg. > - have you used pbc = full for the simulations? > > 1.*The cell length about my PVME model is 4.5 nm which is big enough for > a PVME chain possesses all trans conformation.* Fine, that would be a minimum necessary condition for something that was expected to extend fully. You should actually increase that so that in such a case the opposite ends can't see each other. You need margins at least as large as your largest cut-offs. You can see if this is a potential problem by seeing if any of your monomers do extend in this way. Your experimental system probably had room for about 10^8 such chains end to end, so there is a chance you're comparing apples and oranges here. > *2. The Rg is anaylzed by my own program, which has been validated.* > ** > *3.PBC=XYZ* Has this force field been demonstrated to be effective for this sort of simulation? If not, maybe you've begun to demonstrate that it isn't? Mark From chris.neale at utoronto.ca Tue Sep 19 05:29:13 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Mon, 18 Sep 2006 23:29:13 -0400 Subject: [gmx-users] single and double Message-ID: <20060918232913.fitp9p7aok08kccg@webmail.utoronto.ca> My system here is an opls-aa protein in a POPE/DMPE membrane with tip4p waters. Prior to adding counterions, grompp yields a net charge of -1.999973 and grompp_d yields -2.0. Once I have added counterions, both single and double precision don't give me a warning about a net charge on the system. Either system runs fine for many ns and they don't crash. 1. Is the net charge really as close to 0.0 in the single precision version as it is in the double, or just close enough that there is no warning issued? 2. If single is farther from 0.0, is this a problem? 3. Why does single run faster anyway? I though intel processors treated them the exact same way in terms of the operations that needed to be carried out? Thanks. Chris. From yappik4050 at yahoo.com Tue Sep 19 08:31:31 2006 From: yappik4050 at yahoo.com (Cherry Y. Yates) Date: Mon, 18 Sep 2006 23:31:31 -0700 (PDT) Subject: [gmx-users] periodic boundary condition In-Reply-To: <450A247B.7050608@xray.bmc.uu.se> Message-ID: <20060919063131.44409.qmail@web56906.mail.re3.yahoo.com> Dear David, I tried to use x2top, but it ended up with the following error: 0: GROMOS96 43a1 force field 1: GROMOS96 43b1 vacuum force field 2: GROMOS96 43a2 force field (improved alkane dihedrals) 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 7: [DEPRECATED] Gromacs force field (see manual) 8: [DEPRECATED] Gromacs force field with hydrogens for NMR 9: Encad all-atom force field, using scaled-down vacuum charges 10: Encad all-atom force field, using full solvent charges 0 Looking whether force field file ffG43a1.rtp exists Opening library file /share/apps/gromacs-3.3/share/gromacs/top/ffG43a1.rtp Generating bonds from distances... Opening library file /share/apps/gromacs-3.3/share/gromacs/top/ffG43a1.atp There are 49 type to mass translations atom 438 ------------------------------------------------------- Program x2top, VERSION 3.3 Source code file: futil.c, line: 537 Fatal error: Library file ffG43a1.n2t not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) Could you tell me what is wrong? Many thanks!!! Cherry David van der Spoel wrote: Cherry Y. Yates wrote: > Dear gromacs developers and users, > > I am calculating a nanotube which has periodic boundary condition along > one direction. I wonder how to make an itp file for this system. The > difficulty lies in describing the bond between two end atoms, e.g., two > atoms are bonded in an infinite length system, but are located on the > bottom and top of a unit cell. use x2top and in your mdp file use pbc=full > > Thanks, > > Cherry > > ------------------------------------------------------------------------ > Get your email and more, right on the new Yahoo.com > > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php --------------------------------- Yahoo! Messenger with Voice. Make PC-to-Phone Calls to the US (and 30+ countries) for 2?/min or less. -------------- next part -------------- An HTML attachment was scrubbed... URL: From erikm at xray.bmc.uu.se Tue Sep 19 09:16:48 2006 From: erikm at xray.bmc.uu.se (Erik Marklund) Date: Tue, 19 Sep 2006 09:16:48 +0200 Subject: [gmx-users] bonds In-Reply-To: <97baf6380609181402x5e1736c3g2d5ecf186de63b3e@mail.gmail.com> References: <97baf6380609181402x5e1736c3g2d5ecf186de63b3e@mail.gmail.com> Message-ID: <1158650208.1764.2.camel@jorn.bmc.uu.se> Hi Elias, A more detailed description of the actual error would make it a whole lot easier for us to help out. Perhaps a copy of the actual error message too. /Erik On Mon, 2006-09-18 at 18:02 -0300, Elias santos wrote: > Hi! > I have a question . I am working with a protein that they will count > two > centers FES co-ordinated for cisteins, these cisteins were not on to > iron > atoms, thus I modified the archive itp only with respect the bonds, > no > angles or diedrals, to bind to these two residuos. After the > minimiza??o, I > made one md with restricted position, when I make the total dynamic > with I > tie occurs error in the algorithm shake and it stops in the first > steps > informing that I did not obtain to set molecules of water. I am using > the > field of force of gromacs (option 4) and the water is spc216. > ESS > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Erik Marklund, PhD Student, Molecular Biopcysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 erikm at xray.bmc.uu.se From ababakha at mccammon.ucsd.edu Tue Sep 19 09:26:48 2006 From: ababakha at mccammon.ucsd.edu (Arneh Babakhani) Date: Tue, 19 Sep 2006 00:26:48 -0700 Subject: [gmx-users] make_hole vs. genconf In-Reply-To: <20060919063131.44409.qmail@web56906.mail.re3.yahoo.com> References: <20060919063131.44409.qmail@web56906.mail.re3.yahoo.com> Message-ID: <450F9BB8.1020708@mccammon.ucsd.edu> Dear GMX Users, I'd like to build some lipids around a peptide. Can I do so using genconf? (I know genconf can be used to build a membrane. I'm asking if genconf can be used to build a membrane around a solute, like a transmembrane protein?) I'm also aware of the make_hole tool. My question here is: Does make_hole create a hole of specified dimensions and orientation, according to the solute coordinates? And can you specify exactly where in the membrane you want the whole? So basically what I'm asking is: If you want to make a starting structure (or several structures) with the solute (a peptide) in a specific part of the membrane, is it better to set the desired coordinates of the peptide first and then build a membrane around it? Or, is it wiser to start with an equilibrated membrane and use make_hole to create your hole first at the desired coordinates, then insert the peptide? Thanks, Arneh From prasad.gajula at uni-osnabrueck.de Tue Sep 19 11:16:28 2006 From: prasad.gajula at uni-osnabrueck.de (Prasad Gajula) Date: Tue, 19 Sep 2006 11:16:28 +0200 (CEST) Subject: [gmx-users] Re: velocities (gmx-users Digest, Vol 29, Issue 60) In-Reply-To: <20060919020006.2966E2407B@xray.bmc.uu.se> References: <20060919020006.2966E2407B@xray.bmc.uu.se> Message-ID: <4455.131.173.9.60.1158657388.squirrel@webmail.rz.uni-osnabrueck.de> Thanks for your answer. I hope I did not catch your points well. So, you mean I can use 'gen_vel = no' for the md runs (MD without position restraints, after the completion of PR run with position restarints) my procedure as follows...... EM ---> PR(300ps @ 300K) ----> MD (30ps @ 80K. no postion restraints)---> MD (30 ps @ 100K, no postion restraints ) ---> MD (30 ps @ 200K, no postion restraints) ----> relaxation MD(250ps @ 300K, no postion restraints) ----> final MD (300K, no postion restraints) After Energy minimization, I apply position restarints and generate new velocities at 300K. I take the output of PR run as input to the next MD run which started at 80K ( no position restraints from now). And also from here onwards i dont generate any new velocities, but with the velocities which are written in the previous runs. Please let me know if iam correct or not. Thanks again Gajula > Dear Gromacs Users, > > I am getting different results for simulations with " gen_vel=yes" and > "gen_vel= no". This is expected. No two simulations will be the same unless you run then on the same hardware with exactly the same inputs. gen_vel requires the use of a random number seed. What you want to do, is after equilibration, be sampling from the correct ensemble. > I have generated velocities only for PR MD at 300K. after that I set ' > gen_vel= no ' in mdp file. After the position restrained MD , I slowly > increased the temparature from 80K , 100K , 200K and last 300K. (with > 'gen_vel=no' for all MD) > Is it correct? Because I read both 'yes' and 'no' as possibilites in some > references. Iam bit confused which to use for exact simulations. Personally, I don't think the practice of velocity reassignment in incremental heating while using position restraints is demonstrably better than not using reassignment in incremental heating. Mark From prasad.gajula at uni-osnabrueck.de Tue Sep 19 11:18:11 2006 From: prasad.gajula at uni-osnabrueck.de (Prasad Gajula) Date: Tue, 19 Sep 2006 11:18:11 +0200 (CEST) Subject: [gmx-users] Re:velocities Message-ID: <4458.131.173.9.60.1158657491.squirrel@webmail.rz.uni-osnabrueck.de> Thanks for your answer. I hope I did not catch your points well. So, you mean I can use 'gen_vel = no' for the md runs (MD without position restraints, after the completion of PR run with position restarints) my procedure as follows...... EM ---> PR(300ps @ 300K) ----> MD (30ps @ 80K. no postion restraints)---> MD (30 ps @ 100K, no postion restraints ) ---> MD (30 ps @ 200K, no postion restraints) ----> relaxation MD(250ps @ 300K, no postion restraints) ----> final MD (300K, no postion restraints) After Energy minimization, I apply position restarints and generate new velocities at 300K. I take the output of PR run as input to the next MD run which started at 80K ( no position restraints from now). And also from here onwards i dont generate any new velocities, but with the velocities which are written in the previous runs. Looking forward for your reply. Please let me know Thanks again Gajula > Dear Gromacs Users, > > I am getting different results for simulations with " gen_vel=yes" and > "gen_vel= no". This is expected. No two simulations will be the same unless you run then on the same hardware with exactly the same inputs. gen_vel requires the use of a random number seed. What you want to do, is after equilibration, be sampling from the correct ensemble. > I have generated velocities only for PR MD at 300K. after that I set ' > gen_vel= no ' in mdp file. After the position restrained MD , I slowly > increased the temparature from 80K , 100K , 200K and last 300K. (with > 'gen_vel=no' for all MD) > Is it correct? Because I read both 'yes' and 'no' as possibilites in some > references. Iam bit confused which to use for exact simulations. Personally, I don't think the practice of velocity reassignment in incremental heating while using position restraints is demonstrably better than not using reassignment in incremental heating. Mark From steletch at jouy.inra.fr Tue Sep 19 11:22:12 2006 From: steletch at jouy.inra.fr (=?ISO-8859-1?Q?St=E9phane_T=E9letch=E9a?=) Date: Tue, 19 Sep 2006 11:22:12 +0200 Subject: [gmx-users] single and double In-Reply-To: <20060918232913.fitp9p7aok08kccg@webmail.utoronto.ca> References: <20060918232913.fitp9p7aok08kccg@webmail.utoronto.ca> Message-ID: <450FB6C4.2080409@jouy.inra.fr> chris.neale at utoronto.ca a ?crit : > My system here is an opls-aa protein in a POPE/DMPE membrane with tip4p > waters. > > Prior to adding counterions, grompp yields a net charge of -1.999973 and > grompp_d yields -2.0. Once I have added counterions, both single and > double precision don't give me a warning about a net charge on the > system. Either system runs fine for many ns and they don't crash. > > 1. Is the net charge really as close to 0.0 in the single precision > version as it is in the double, or just close enough that there is no > warning issued? The net charge is really close to zero, the difference may rely on hardware roundoff, and on the topology limits (charge precision on each atom/group). This is why you see the difference between single and double precision. > 2. If single is farther from 0.0, is this a problem? It depends :-) I assume you're using PME, in this case, the system will be scaled to 0 and for you run, that won't be a problem (since spreading a <1e-4 charges among >100 000 atoms won't interfere much with their net charge ...) and the roundoff errors due to the calculations themselves are bigger than this single vs double difference. > 3. Why does single run faster anyway? I though intel processors treated > them the exact same way in terms of the operations that needed to be > carried out? It depends of the hardware you're talking about. On single precision systems, the run would run at the same speed on 32 bits architecture and on 64 bits architectures. On double precision systems, the same run will take twice the time on 32 bits than on 64bits (roughly). Globally, single precision == 32bits, double precision == 64bits. That means on single precision run on 32bits machines will be done in the same time that double precision on 64bits (roughly again). This is more or less true with gromacs since processors have more than two types of calculation units (thinkk of sse, sse2, 3Dnowext, ...) and gromacs is able to take most of them (if not all) into account via specialized routines, but that the goal. > Thanks. > Chris. Cheers, St?phane -- St?phane T?letch?a, PhD. http://www.steletch.org Unit? Math?matique Informatique et G?nome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert T?l : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901 From tsjerkw at gmail.com Tue Sep 19 15:07:23 2006 From: tsjerkw at gmail.com (Tsjerk Wassenaar) Date: Tue, 19 Sep 2006 15:07:23 +0200 Subject: [gmx-users] protein unstable for parallel job while stable for serial one In-Reply-To: <20060918152147.38989.qmail@web60811.mail.yahoo.com> References: <20060918152147.38989.qmail@web60811.mail.yahoo.com> Message-ID: <8ff898150609190607x3c0cf39n745324cfe6d56c31@mail.gmail.com> Hi Akansha, Either you need to simulate both systems until you have full convergence before you can make conclusions regarding the (dis)similar behaviour or you have to test consistently, running replicate simulations both on one processor and on 16. That being said, it is very well possible that even between two simulations of the same system under completely identical conditions, except for the starting velocities and possibly the exact starting structure, you will get two completely different results. If you're protein can undergo a conformational change it's basically a matter of chance whether you observe it or not. Of course, I don't say it is not related to your simulation being distributed over multiple processors. It may be, but in order to exclude other effects you have to repeat simulations and/or work through the code very carefully. Which version of Gromacs did you use? Hope it helps, Tsjerk On 9/18/06, Akansha Saxena wrote: > Hello > > Has anybody seen a protein becoming unstable on > parallel nodes while remaining stable on single node? > > I am running a NPT molecular dynamics simulation. The > system contains a protein with 141 residues surrounded > by water making the total to 32714 atoms. I ran this > simulation at two places for 8ns. One as a serial job > and the other as a parallel job on 16 nodes. > > The protein remains stable all through for the serial > job but for parallel job the protein opens up after > 3ns of simulation and is never stable after that. > > All other conditions are exactly the same. Any help > would be highly appreciated. > > Akansha > > > > Akansha Saxena > Graduate Student > Department of Biomedical Engineering > Washington University in St Louis > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 From asaxena17 at yahoo.com Tue Sep 19 16:58:27 2006 From: asaxena17 at yahoo.com (Akansha Saxena) Date: Tue, 19 Sep 2006 07:58:27 -0700 (PDT) Subject: [gmx-users] Re: protein unstable for parallel job while stable for serial one Message-ID: <20060919145827.83981.qmail@web60824.mail.yahoo.com> Hi Tsjerk, >Hi Akansha, >Either you need to simulate both systems until you >have full >convergence before you can make conclusions regarding >the (dis)similar behaviour Well I can simulate it until convergence but that on a single processor for my system will take several months of computer time. >or you have to test consistently, running replicate >simulations both on one processor and on 16. This is what I was doing. I was running exactly identical simulations on 1 processor and on 16 processors. By identical i mean - same starting structure, velocities taken from the same *.trr file. The only difference was the number of nodes for the production run. >That being said, it is very well possible that even >between two >simulations of the same system under completely >identical conditions, >except for the starting velocities and possibly the >exact starting >structure, you will get two completely different >results. If you're >protein can undergo a conformational change it's >basically a matter of >chance whether you observe it or not. But I give the same velocities and use exactly same starting structure for both simulations. Basically I use the same files for both cases. Only difference lying in the number of processors. I would think that with same intial conditions the calculations should be identical for both cases. >Of course, I don't say it is not related to your >simulation being >distributed over multiple processors. It may be, but >in order to >exclude other effects you have to repeat simulations >and/or work >through the code very carefully. Which version of >Gromacs did you use? I am using Gromacs3.3. It would very helpful if you can please suggest what care should I take in order to exclude other effects when I repeat the simulation. Thanx Akansha >Hope it helps, > >Tsjerk >On 9/18/06, Akansha Saxena >wrote: >> Hello >> >> Has anybody seen a protein becoming unstable on >> parallel nodes while remaining stable on single >>node? >> >> I am running a NPT molecular dynamics simulation. >>The system contains a protein with 141 residues >>surrounded >> by water making the total to 32714 atoms. I ran this >> simulation at two places for 8ns. One as a serial >>job >> and the other as a parallel job on 16 nodes. >> >> The protein remains stable all through for the >>serial >> job but for parallel job the protein opens up after >> 3ns of simulation and is never stable after that. >> >> All other conditions are exactly the same. Any help >> would be highly appreciated. >> >> Akansha >> >> >> >> Akansha Saxena >> Graduate Student >> Department of Biomedical Engineering >> Washington University in St Louis >> >> gmx-users mailing list gmx-users at gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please don't post (un)subscribe requests to the >>list. Use the >> www interface or send it to gmx-users-request at >>gromacs.org. >> Can't post? Read >>http://www.gromacs.org/mailing_lists/users.php >> >-- >Tsjerk A. Wassenaar, Ph.D. >Groningen Biomolecular Sciences and Biotechnology >Institute (GBB) >Dept. of Biophysical Chemistry >University of Groningen >Nijenborgh 4 >9747AG Groningen, The Netherlands >+31 50 363 4336 Akansha Saxena Graduate Student Department of Biomedical Engineering Washington University in St Louis __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From Mark.Abraham at anu.edu.au Tue Sep 19 17:12:10 2006 From: Mark.Abraham at anu.edu.au (Mark Abraham) Date: Wed, 20 Sep 2006 01:12:10 +1000 Subject: [gmx-users] Re: protein unstable for parallel job while stable for serial one In-Reply-To: <20060919145827.83981.qmail@web60824.mail.yahoo.com> References: <20060919145827.83981.qmail@web60824.mail.yahoo.com> Message-ID: <451008CA.2050609@anu.edu.au> Akansha Saxena wrote: > This is what I was doing. I was running exactly > identical simulations on 1 processor and on 16 > processors. > By identical i mean - same starting structure, > velocities taken from the same *.trr file. The only > difference was the number of nodes for the production > run. Well this sounds sensible, so long as you weren't doing an erroneous gen_vel = yes. > But I give the same velocities and use exactly same > starting structure for both simulations. Basically I > use the same files for both cases. Only difference > lying in the number of processors. > I would think that with same intial conditions the > calculations should be identical for both cases. Real-world floating point computations are not algebraic computations. You can divide a number n by x, and add the result to itself x times, and a test for equality against n will fail, for sufficiently pathological n and x. The order in which summation occurs when you have a mixture of large and small numbers can also affect the result through accumulated round-off errors. A parallel computation will effectively be doing this. The fact this happens is not actually a problem - the perturbation is not so large you are sampling a different ensemble. You just don't have algebraic reproducibility. Mark From N.Goga at rug.nl Tue Sep 19 16:35:08 2006 From: N.Goga at rug.nl (N.Goga) Date: Tue, 19 Sep 2006 16:35:08 +0200 Subject: [gmx-users] Co-variance Analysis In-Reply-To: <8ff898150609190607x3c0cf39n745324cfe6d56c31@mail.gmail.com> References: <20060918152147.38989.qmail@web60811.mail.yahoo.com> <8ff898150609190607x3c0cf39n745324cfe6d56c31@mail.gmail.com> Message-ID: Hi Tsjerk, thank you for your help for the generation of the files. I found them. Please can you help me with some litle bit more information. 1) How many atoms did you used ?(it seems 1894 looking to the nr. of lines of the masses) 2) Are just normal masses or did you compute (mass_particle)^(1/2) 3) How many frames of the positions the particles are used? 4) How many eigenvalues in average are needed (the order of magnitude) for such a co-variance computation? Thank you in advance for your answer. Best regards Nicu From chris.neale at utoronto.ca Tue Sep 19 19:09:41 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Tue, 19 Sep 2006 13:09:41 -0400 Subject: [gmx-users] make_hole vs. genconf Message-ID: <20060919130941.phj3f2vs9ri8ssk0@webmail.utoronto.ca> > I'd like to build some lipids around a peptide. Can I do so using > genconf? (I know genconf can be used to build a membrane. I'm > asking if genconf can be used to build a membrane around a solute, > like a transmembrane protein?) "around"? No. > I'm also aware of the make_hole tool. My question here is: Does > make_hole create a hole of specified dimensions and orientation, > according to the solute coordinates? And can you specify exactly > where in the membrane you want the whole? Make_hole doesn't actually make a hole. You need to make the premilinary hole yourself. The general problem is that if you take out all lipids that contact the protein, then you will have a huge vaccuum aroung the protein. So first you take out all the lipids whose headgroup clashed (manually) then run make_hole to bend the tails out of the space that is to be occupied by the protein, then add the protien. You will need to install gromacs-3.1.4 to do this. > So basically what I'm asking is: If you want to make a starting > structure (or several structures) with the solute (a peptide) in a > specific part of the membrane, is it better to set the desired > coordinates of the peptide first and then build a membrane around > it? Or, is it wiser to start with an equilibrated membrane and use > make_hole to create your hole first at the desired coordinates, then > insert the peptide? 1. Build your membrane (or find coords somewhere) 2. equilibrate it 3. Use make_hole or inflategro (I have never tried this one) http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis 4. re-equilibrate Reason not to do it all at once is because you want to limit your protein's exposure to vaccuum, although I suppose you could use position restraints to solve this issue (heavy atom on the protein and a z-only on the lipid phosphate). Chris From anoddlad at yahoo.com Tue Sep 19 19:35:22 2006 From: anoddlad at yahoo.com (Alan Dodd) Date: Tue, 19 Sep 2006 10:35:22 -0700 (PDT) Subject: [gmx-users] make_hole vs. genconf In-Reply-To: <20060919130941.phj3f2vs9ri8ssk0@webmail.utoronto.ca> Message-ID: <20060919173522.53941.qmail@web39107.mail.mud.yahoo.com> > > > I'm also aware of the make_hole tool. My question > here is: Does > > make_hole create a hole of specified dimensions > and orientation, > > according to the solute coordinates? And can you > specify exactly > > where in the membrane you want the whole? > > Make_hole doesn't actually make a hole. You need to > make the > premilinary hole yourself. Not true, I've made a hole using make_hole. Manually removing central lipids, and using make_hole to finess the rim of the hole is probably more computationally efficient, but make_hole is perfectly capable of doing what the name says (and less labor intensive). __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From sir_donald_bradman at yahoo.com Tue Sep 19 19:48:21 2006 From: sir_donald_bradman at yahoo.com (Manohar Murthi) Date: Tue, 19 Sep 2006 10:48:21 -0700 (PDT) Subject: [gmx-users] umbrella sampling pull.pdo output In-Reply-To: <20060919092153.F01CB24080@xray.bmc.uu.se> Message-ID: <20060919174822.83430.qmail@web51010.mail.yahoo.com> hi everyone i'm trying to calculate the free energy of binding of a guest and host in solution by umbrella sampling. my pull groups consist of individual atoms on the host and guest. i tried a force constant of 1/100*single bond strength. when the umbrella distance between the host and guest atoms is set to {0.4,0.4,0.4} (i.e. .4 nm separation in x,y, &z), i notice that the pull.pdo file eventually shows the separations in x,y,&z becoming very small - on the order of 0.02nm, which should surely result in an energy explosion. however, a 100ps simulation runs to completion with no complaints. examining the distance between the 2 pulled atoms using g_bond shows that they in fact remain around 0.7nm (=sqrt(3*.4^2)) apart, as expected. visual inspection of the trajectory confirms that the pulled atoms don't approach each other too closely. is this perchance a bug or am i doing something wrong? i start the simulation from a random configuration selected from a long unconstrained nvt run using grompp -f umbrella.mdp -o u4 -t nvt1.trr -time 100 -n index.ndx (where index.ndx defines energy groups), then run using mdrun -s u4.trr -pi pull.ppa -pd u4 -pn pull.ndx. my pull.ppa file looks like this: verbose = yes runtype = umbrella reference_group = zn152 group1 = n204 reftype = com k1 = 4393.2 pos1 = 0.4 0.4 0.4 and pull.ndx is: [ zn152 ] 152 [ n204 ] 204 please let me know if more information is required to understand the problem. any suggestions would be greatly appreciated. thanks mo ps - i also get an error running g_bond: Fatal error: No distribution....(i0 = 999, i1 = 1)? ? ! ! ? ! with no histogram being output. i thought this may be to do with the fact that the atoms aren't bonded, but have yet to check on this. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From MichaelOwen at creighton.edu Tue Sep 19 19:46:34 2006 From: MichaelOwen at creighton.edu (Owen, Michael) Date: Tue, 19 Sep 2006 12:46:34 -0500 Subject: [gmx-users] VAL group Message-ID: <80C4D42673F70F4B9333B9F3AFFCC5081D881C@EXBE06.blue.jays.creighton.edu> Hello gmx users, when I convert a pdb file of a peptide that contains a valyl residue into a .gro file a separate "group" is made for the atoms in the valyl residue. This has happened when OPLSAA/l and the GROMOS96 53a6 force fields were used. The molecule appears as one in the topology file, and the atomic description of the valyl residue in the pdb file matches that of the ffoplsa.rtp file. Could something be wrong with the pdb2gmx program? Thank you in advance for any suggestions. Sincerely, Michael Owen -------------- next part -------------- An HTML attachment was scrubbed... URL: From ababakha at mccammon.ucsd.edu Tue Sep 19 21:30:15 2006 From: ababakha at mccammon.ucsd.edu (Arneh Babakhani) Date: Tue, 19 Sep 2006 12:30:15 -0700 Subject: [gmx-users] make_hole vs. genconf In-Reply-To: <20060919130941.phj3f2vs9ri8ssk0@webmail.utoronto.ca> References: <20060919130941.phj3f2vs9ri8ssk0@webmail.utoronto.ca> Message-ID: <45104547.2030307@mccammon.ucsd.edu> Great, thanks Chris! chris.neale at utoronto.ca wrote: >> I'd like to build some lipids around a peptide. Can I do so using >> genconf? (I know genconf can be used to build a membrane. I'm >> asking if genconf can be used to build a membrane around a solute, >> like a transmembrane protein?) > > "around"? No. > >> I'm also aware of the make_hole tool. My question here is: Does >> make_hole create a hole of specified dimensions and orientation, >> according to the solute coordinates? And can you specify exactly >> where in the membrane you want the whole? > > Make_hole doesn't actually make a hole. You need to make the > premilinary hole yourself. The general problem is that if you take out > all lipids that contact the protein, then you will have a huge vaccuum > aroung the protein. So first you take out all the lipids whose > headgroup clashed (manually) then run make_hole to bend the tails out > of the space that is to be occupied by the protein, then add the protien. > > You will need to install gromacs-3.1.4 to do this. > >> So basically what I'm asking is: If you want to make a starting >> structure (or several structures) with the solute (a peptide) in a >> specific part of the membrane, is it better to set the desired >> coordinates of the peptide first and then build a membrane around >> it? Or, is it wiser to start with an equilibrated membrane and use >> make_hole to create your hole first at the desired coordinates, then >> insert the peptide? > > 1. Build your membrane (or find coords somewhere) > 2. equilibrate it > 3. Use make_hole or inflategro (I have never tried this one) > http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis > 4. re-equilibrate > > Reason not to do it all at once is because you want to limit your > protein's exposure to vaccuum, although I suppose you could use > position restraints to solve this issue (heavy atom on the protein and > a z-only on the lipid phosphate). > > Chris > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use thewww > interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > From tsjerkw at gmail.com Tue Sep 19 23:30:51 2006 From: tsjerkw at gmail.com (Tsjerk Wassenaar) Date: Tue, 19 Sep 2006 23:30:51 +0200 Subject: [gmx-users] Re: protein unstable for parallel job while stable for serial one In-Reply-To: <451008CA.2050609@anu.edu.au> References: <20060919145827.83981.qmail@web60824.mail.yahoo.com> <451008CA.2050609@anu.edu.au> Message-ID: <8ff898150609191430g44249e2cl87bd0494629fc783@mail.gmail.com> Hi Akansha (and Mark), The approach taken is indeed sensible, and in addition to that I fully support the comments made by Mark. It's actually part of what I meant, changing the number of processors gives you a difference between your simulations. However, it should not give you a consistent difference. That is, if you perform, say 100 simulations on 1 processor and 100 on 16, the results from one set should be similar to those obtained from the other. In casu, you should observe the conformational change approximately an equal number of times. The same would hold for full convergence of your system. In that case, the number of transitions (folding/unfolding, conformational change) should be approximately equal over a certain time and have the same rate, duration, etc. You'll only be able to get that for small systems. It is possible that the division over multiple processors introduces some artefacts, which was in fact found by Jelger Risselada some while ago (you can check the mailinglist archive). But I think this bug was fixed. You might be able to detect such a consistent effect in the results if you perform say five simulations on 1 processor and five on 16 processors, using different starting velocities. I hope this helps you a bit further. Best regards, Tsjerk On 9/19/06, Mark Abraham wrote: > Akansha Saxena wrote: > > This is what I was doing. I was running exactly > > identical simulations on 1 processor and on 16 > > processors. > > By identical i mean - same starting structure, > > velocities taken from the same *.trr file. The only > > difference was the number of nodes for the production > > run. > > Well this sounds sensible, so long as you weren't doing an erroneous > gen_vel = yes. > > > But I give the same velocities and use exactly same > > starting structure for both simulations. Basically I > > use the same files for both cases. Only difference > > lying in the number of processors. > > I would think that with same intial conditions the > > calculations should be identical for both cases. > > Real-world floating point computations are not algebraic computations. > You can divide a number n by x, and add the result to itself x times, > and a test for equality against n will fail, for sufficiently > pathological n and x. The order in which summation occurs when you have > a mixture of large and small numbers can also affect the result through > accumulated round-off errors. A parallel computation will effectively be > doing this. The fact this happens is not actually a problem - the > perturbation is not so large you are sampling a different ensemble. You > just don't have algebraic reproducibility. > > Mark > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 From Mark.Abraham at anu.edu.au Wed Sep 20 02:26:54 2006 From: Mark.Abraham at anu.edu.au (Mark Abraham) Date: Wed, 20 Sep 2006 10:26:54 +1000 Subject: [gmx-users] VAL group In-Reply-To: <80C4D42673F70F4B9333B9F3AFFCC5081D881C@EXBE06.blue.jays.creighton.edu> References: <80C4D42673F70F4B9333B9F3AFFCC5081D881C@EXBE06.blue.jays.creighton.edu> Message-ID: <45108ACE.4010706@anu.edu.au> Owen, Michael wrote: > > Hello gmx users, > > when I convert a pdb file of a peptide that contains a valyl residue > into a .gro file a separate "group" is made for the atoms in the valyl > residue. In what sense...? please include a relevant file excerpt, and the commands that created it. > This has happened when OPLSAA/l and the GROMOS96 53a6 force > fields were used. The molecule appears as one in the topology file, > and the atomic description of the valyl residue in the pdb file matches > that of the ffoplsa.rtp file. Have these forcefields really being modified for a radical, or are you really describing a valine residue? Mark From jiqing at iccas.ac.cn Wed Sep 20 03:34:16 2006 From: jiqing at iccas.ac.cn (=?gb2312?B?1vfUwiCjuqOp?=) Date: Wed, 20 Sep 2006 09:34:16 +0800 Subject: [gmx-users] Re: The molecule size (jiqing) Message-ID: <000f01c6dc54$e2a11950$851ae29f@jiqing> ?Has this force field been demonstrated to be effective >for this sort of >simulation? If not, maybe you've begun to demonstrate >that it isn't? >Mark Yes , you are quite right. In GMX manual 3.2, at the end of chapter 4, it was said that gromos96 is not, however, recommended for use with long alkanes and lipids. So user has to validate force parameters. Now the problem is for a periodic boundary system, the density is ok but the Rg is too small. I feel the parameters for proper dihedrals need to be improved. Is it right? ************************************************* Ji Qing Institute of Chemistry, Chinese Academy of Sciences Tel: 0086-10-62562894 ?82618423 ************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From Mark.Abraham at anu.edu.au Wed Sep 20 04:47:04 2006 From: Mark.Abraham at anu.edu.au (Mark Abraham) Date: Wed, 20 Sep 2006 12:47:04 +1000 Subject: [gmx-users] Re: The molecule size (jiqing) In-Reply-To: <000f01c6dc54$e2a11950$851ae29f@jiqing> References: <000f01c6dc54$e2a11950$851ae29f@jiqing> Message-ID: <4510ABA8.6050704@anu.edu.au> ?? ?? wrote: > > ?Has this force field been demonstrated to be effective >for this sort of > >simulation? If not, maybe you've begun to demonstrate >that it isn't? > > >Mark > > Yes , you are quite right. In GMX manual 3.2, at the end of chapter 4, > it was said that gromos96 is not, however, recommended for use with long > alkanes and lipids. > So user has to validate force parameters. Now the problem is for a > periodic boundary system, the density is ok but the Rg is too small. I > feel the parameters for proper dihedrals need to be improved. Is it right? It's likely that nobody knows. Find a force field that does work for such simulations, or read everything you can find on how to build force fields and do it from scratch. Modifying one sort of parameter is like taking a Beethoven symphony and substituting the second violin part with bass guitar line from "Smoke on the Water". It might work, but you'd be mad to bet on it. Mark From jellby at yahoo.com Wed Sep 20 09:25:17 2006 From: jellby at yahoo.com (=?iso-8859-1?q?Ignacio=20Fern=E1ndez=20Galv=E1n?=) Date: Wed, 20 Sep 2006 08:25:17 +0100 (BST) Subject: [gmx-users] Free energy for charged molecules Message-ID: <20060920072517.38044.qmail@web33008.mail.mud.yahoo.com> Hi all, Is there some precaution or additional term I should take into account when calculating the free energy of solvation for a charged molecule? I plan to make the molecule "disappear" whith lambda moving from 0 to 1 and then perform a thermodynamical integration, this seems to work reasonably well for neutral molecules. Is there any "gotcha" with charged molecules? Of course, I'm using PME, pbc=xyz and a large enough simulation box. Thanks ___________________________________________________________ To help you stay safe and secure online, we've developed the all new Yahoo! Security Centre. http://uk.security.yahoo.com From alokjain at iitk.ac.in Wed Sep 20 09:50:45 2006 From: alokjain at iitk.ac.in (Alok) Date: Wed, 20 Sep 2006 13:20:45 +0530 Subject: [gmx-users] 1-4 columb interaction Message-ID: <001c01c6dc89$7ad0eaa0$65741aac@alok> Dear All, Is there any scaling for 1-4 columb interaction in gromacs force field if yes then how? is it also like LJ14 which uses separate set of parameters for 1-4 interaction? Manual only talked about separate parameters for LJ14 specifically for repulsion term, but in mailing list it was mentioned that there is always scaling for Columb-14 but how I am not able to get? Regards, Alok -------------- next part -------------- An HTML attachment was scrubbed... URL: From jake at ncsa.uiuc.edu Wed Sep 20 13:37:20 2006 From: jake at ncsa.uiuc.edu (Eric Jakobsson) Date: Wed, 20 Sep 2006 06:37:20 -0500 Subject: [gmx-users] hydrocarbon force fields In-Reply-To: <4510ABA8.6050704@anu.edu.au> References: <000f01c6dc54$e2a11950$851ae29f@jiqing> <4510ABA8.6050704@anu.edu.au> Message-ID: <7.0.0.16.2.20060920063627.04b96c18@ncsa.uiuc.edu> For hydrocarbon force fields, see: Chiu, S. W., Clark, M. M., Jakobsson, E., Subramaniam, S., and H. L. Scott. 1999b. Optimizations of hydrocarbon chain interaction parameters: Application to the simulation of fluid phase lipid bilayers. J. Phys. Chem. B 103:6323-6327 At 09:47 PM 9/19/2006, you wrote: >???? ???? wrote: > > > > ??Has this force field been demonstrated to be effective >for this sort of > > >simulation? If not, maybe you've begun to demonstrate >that it isn't? > > > > >Mark > > > > Yes , you are quite right. In GMX manual 3.2, at the end of chapter 4, > > it was said that gromos96 is not, however, recommended for use with long > > alkanes and lipids. > > So user has to validate force parameters. Now the problem is for a > > periodic boundary system, the density is ok but the Rg is too small. I > > feel the parameters for proper dihedrals need to be improved. Is it right? > >It's likely that nobody knows. > >Find a force field that does work for such simulations, or read >everything you can find on how to build force fields and do it from >scratch. Modifying one sort of parameter is like taking a Beethoven >symphony and substituting the second violin part with bass guitar line >from "Smoke on the Water". It might work, but you'd be mad to bet on it. > >Mark >_______________________________________________ >gmx-users mailing list gmx-users at gromacs.org >http://www.gromacs.org/mailman/listinfo/gmx-users >Please don't post (un)subscribe requests to the list. Use the >www interface or send it to gmx-users-request at gromacs.org. >Can't post? Read http://www.gromacs.org/mailing_lists/users.php --------------------------------- Eric Jakobsson, Ph.D. Professor, Department of Molecular and Integrative Physiology, and of Biochemistry, and of the Center for Biophysics and Computational Biology Senior Research Scientist, National Center for Supercomputing Applications Professor, Beckman Institute for Advanced Science and Technology 3261 Beckman Institute, mc251 University of Illinois, Urbana, IL 61801 ph. 217-244-2896 fax 217-244-2909 -------------- next part -------------- An HTML attachment was scrubbed... URL: From qiaobf at gmail.com Wed Sep 20 14:13:50 2006 From: qiaobf at gmail.com (Qiao Baofu) Date: Wed, 20 Sep 2006 14:13:50 +0200 Subject: [gmx-users] question about energy and pressure Message-ID: <6a91f07b0609200513g5c404d49gd5e5e8f784afd0b6@mail.gmail.com> Hi all, I have some questions about the gromacs: 1. I simualted a pure small molecule system. All the simulation is ok. But when I use g_energy to calculate the energy of bond, angle, lj, and coloumb, it gives the following energy. The energies is much bigger, about 50-100 times bigger than the reported data. What's wrong? Statistics over 5000001 steps [ 0.0000 thru 5000.0000 ps ], 6 data sets Energy Average RMSD Fluct. Drift Tot-Drift ------------------------------------------------------------------------------- Bond 2869.13 93.6564 93.6562 0.000137548 0.687742 Angle 7303.46 140.13 140.13 0.000189867 0.949334 Ryckaert-Bell. 3326.2 97.6245 97.6161 -0.000890977 -4.45489 LJ-(SR) -7616.62 138.684 138.67 -0.00138166 - 6.90831 Coulomb-(SR) -22763.2 138.465 138.238 -0.00549019 -27.451 Potential -64743 219.54 219.203 -0.00842365 - 42.1182 2. I used the "isotropic!!" pressure coupling, but at the end of the .log file (in the average section), it says: Pressure (bar) -2.64364e+01 3.71622e+01 3.00738e+00 3.71622e+01 1.32932e+01 -2.49814e+01 3.00738e+00 -2.49814e+01 1.61609e+01 The Pxx, Pyy, Pzz are not equal. Why? Sincerely yours, ********************************************** Baofu Qiao, PhD Frankfurt Institute for Advanced Studies Max-von-Laue-Str. 1 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From qiaobf at gmail.com Wed Sep 20 15:47:31 2006 From: qiaobf at gmail.com (Qiao Baofu) Date: Wed, 20 Sep 2006 15:47:31 +0200 Subject: [gmx-users] 1-4 columb interaction In-Reply-To: <001c01c6dc89$7ad0eaa0$65741aac@alok> References: <001c01c6dc89$7ad0eaa0$65741aac@alok> Message-ID: <6a91f07b0609200647n4152aa1fu711c2d455987ccb8@mail.gmail.com> In the force field file ff***.itp, there are two terms to scale lj and coloumb after the option: generating pairs. 2006/9/20, Alok : > > Dear All, > > Is there any scaling for 1-4 columb interaction in gromacs force field if > yes then how? is it also like LJ14 which uses separate set of parameters for > 1-4 interaction? > > Manual only talked about separate parameters for LJ14 specifically for > repulsion term, but in mailing list it was mentioned that there is always > scaling for Columb-14 but how I am not able to get? > > Regards, > Alok > > > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- Sincerely yours, ********************************************** Baofu Qiao, PhD Frankfurt Institute for Advanced Studies Max-von-Laue-Str. 1 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From alokjain at iitk.ac.in Wed Sep 20 16:09:07 2006 From: alokjain at iitk.ac.in (Alok) Date: Wed, 20 Sep 2006 19:39:07 +0530 Subject: [gmx-users] 1-4 columb interaction References: <001c01c6dc89$7ad0eaa0$65741aac@alok> <6a91f07b0609200647n4152aa1fu711c2d455987ccb8@mail.gmail.com> Message-ID: <002601c6dcbe$563022d0$65741aac@alok> Thanks Qiao for your reply. But If I am using genpair = no (GROMOS 96 force field) then there is no meaning of fudgeLJ and fudgeQQ (correct me if I am wrong). So more specific if I am using GROMOS96 force field then is there any scaling for 1-4 columb interaction?? if yes then how? Regards, Alok ----- Original Message ----- From: Qiao Baofu To: Discussion list for GROMACS users Sent: Wednesday, September 20, 2006 7:17 PM Subject: Re: [gmx-users] 1-4 columb interaction In the force field file ff***.itp, there are two terms to scale lj and coloumb after the option: generating pairs. 2006/9/20, Alok : Dear All, Is there any scaling for 1-4 columb interaction in gromacs force field if yes then how? is it also like LJ14 which uses separate set of parameters for 1-4 interaction? Manual only talked about separate parameters for LJ14 specifically for repulsion term, but in mailing list it was mentioned that there is always scaling for Columb-14 but how I am not able to get? Regards, Alok _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Sincerely yours, ********************************************** Baofu Qiao, PhD Frankfurt Institute for Advanced Studies Max-von-Laue-Str. 1 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ********************************************** ------------------------------------------------------------------------------ _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -------------- next part -------------- An HTML attachment was scrubbed... URL: From fujisaki at bu.edu Wed Sep 20 16:07:03 2006 From: fujisaki at bu.edu (Hiroshi Fujisaki) Date: Wed, 20 Sep 2006 10:07:03 -0400 Subject: [gmx-users] Installation of Gromacs into BG/L Message-ID: <20060920100340.A822.FUJISAKI@bu.edu> Dear Gromacs users, I am now trying to install gromacs into our BlueGene facility, but I fail when I do make. (configure seems to be fine.) The link to the FFTW library does not seem to work. I use fftw-2.1.5. I attach the excerpt of the make log file here (the last part of the log). #################################################################################### cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -maltivec -mabi=altivec -mcpu=7450 -mtune=970 -o mdrun glaasje.o gctio.o init_sh.o ionize.o do_gct.o relax_sh.o repl_ex.o xutils.o md.o mdrun.o genalg.o -L/bgl/local/fftw-2.1.5/lib ../mdlib/.libs/libmd_d.a -L/usr/X11R6/lib ../gmxlib/.libs/libgmx_d.a -lnsl /bgl/local/fftw-2.1.5/lib/librfftw.a /bgl/local/fftw-2.1.5/lib/libfftw.a -lm /usr/X11R6/lib/libXm.so -lXt -lSM -lICE -lXext -lXp -lX11 /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x56): In function `read_int': /u/walkup/download/fftw-2.1.5/fftw/wisdom.c:224: undefined reference to `__ctype_b' /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x62):/u/walkup/download/fftw-2.1.5/fftw/wisdom.c:224: undefined reference to `__ctype_b' /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x9e):/u/walkup/download/fftw-2.1.5/fftw/wisdom.c:229: undefined reference to `__ctype_b' /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0xfa): In function `eat_blanks': /u/walkup/download/fftw-2.1.5/fftw/wisdom.c:209: undefined reference to `__ctype_b' /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x102):/u/walkup/download/fftw-2.1.5/fftw/wisdom.c:209: undefined reference to `__ctype_b' /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x126):/u/walkup/download/fftw-2.1.5/fftw/wisdom.c:209: more undefined references to `__ctype_b' follow /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x26a): In function `toupper': /bgl/BlueLight/ppcfloor/blrts-gnu/powerpc-bgl-blrts-gnu/sys-include/ctype.h:176: undefined reference to `__ctype_toupper' /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x276):/bgl/BlueLight/ppcfloor/blrts-gnu/powerpc-bgl-blrts-gnu/sys-include/ctype.h:176: undefined reference to `__ctype_toupper' /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x28e): In function `tolower': /bgl/BlueLight/ppcfloor/blrts-gnu/powerpc-bgl-blrts-gnu/sys-include/ctype.h:170: undefined reference to `__ctype_tolower' /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x29a):/bgl/BlueLight/ppcfloor/blrts-gnu/powerpc-bgl-blrts-gnu/sys-include/ctype.h:170: undefined reference to `__ctype_tolower' /bgl/local/fftw-2.1.5/lib/libfftw.a(rader.o)(.text+0x128): In function `fftwi_twiddle_rader': /u/walkup/download/fftw-2.1.5/fftw/rader.c:273: undefined reference to `__divi64' /bgl/local/fftw-2.1.5/lib/libfftw.a(rader.o)(.text+0x244):/u/walkup/download/fftw-2.1.5/fftw/rader.c:321: undefined reference to `__divi64' /bgl/local/fftw-2.1.5/lib/libfftw.a(rader.o)(.text+0x470): In function `fftw_twiddle_rader': /u/walkup/download/fftw-2.1.5/fftw/rader.c:190: undefined reference to `__divi64' /bgl/local/fftw-2.1.5/lib/libfftw.a(rader.o)(.text+0x590):/u/walkup/download/fftw-2.1.5/fftw/rader.c:238: undefined reference to `__divi64' /bgl/local/fftw-2.1.5/lib/libfftw.a(rader.o)(.text+0x8ac): In function `create_rader_aux': /u/walkup/download/fftw-2.1.5/fftw/rader.c:115: undefined reference to `__divi64' /bgl/local/fftw-2.1.5/lib/libfftw.a(rader.o)(.text+0xa7c):/u/walkup/download/fftw-2.1.5/fftw/rader.c:59: more undefined references to `__divi64' follow collect2: ld returned 1 exit status make[3]: *** [mdrun] Error 1 make[3]: Leaving directory `/project2/gaussden/fujisaki/src/gromacs-3.3.1/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/project2/gaussden/fujisaki/src/gromacs-3.3.1/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/project2/gaussden/fujisaki/src/gromacs-3.3.1/src' make: *** [all-recursive] Error 1 ######################################################################################## I appreciate your help. Best wishes, -- Hiroshi Fujisaki From p.biswas at csuohio.edu Wed Sep 20 17:27:52 2006 From: p.biswas at csuohio.edu (Pradip Kumar Biswas) Date: Wed, 20 Sep 2006 11:27:52 -0400 Subject: [gmx-users] running CPMD with GROMACS interface in SGI irix 6.5 In-Reply-To: <93e2edd90609121810x3631409fy8e44a8a78c346997@mail.gmail.com> References: <93e2edd90609121810x3631409fy8e44a8a78c346997@mail.gmail.com> Message-ID: Hi James, Thanks for reporting the problem. I was out and also could not see mails from this server. I got you mail today and will reply to you asap. Best, Pradip. On Sep 12, 2006, at 9:10 PM, james zhang wrote: > Hi > ? > I got some trouble in running CPMD with GROMACS?interface?in SGI irix > 6.5. Thanks in advance > ? > the error is > > ?[PEAK NUMBER? 116]?????? PEAK MEMORY????? 14169180 =? 113.4 MBytes > ?[ALL. NUMBER? 116]????? TOTAL MEMORY????? 13983696 =? 111.9 MBytes > ?================================================================== > > > ?PROGRAM STOPS IN SUBROUTINE MEMORY_CHECK|? CORRUPTED MEMORY [PROC=?? > 8] > ?EIGV???????? 390897072 CORRUPTED?? 390994624 CORRUPTED?????? 12193 > ?SC0????????? 390994640 CORRUPTED?? 391254032 CORRUPTED?????? 32423 > ?PME????????? 391254048 CORRUPTED?? 391513440 CORRUPTED?????? 32423 > ?GDE????????? 391513456 CORRUPTED?? 391772848 CORRUPTED?????? 32423 > ?HGPOT??????? 391860984 CORRUPTED?? 392180992 CORRUPTED?????? 40000 > ?HIPZ???????? 392181008 CORRUPTED?? 394741016 CORRUPTED????? 320000 > ?NZFFP??????? 394741032 CORRUPTED?? 396297320 CORRUPTED????? 194535 > ?NZFSP??????? 396297336 CORRUPTED?? 396987776 CORRUPTED?????? 86304 > ??? 396987792 CORRUPTED?? 403238296 CORRUPTED????? 781312 > ??? 403238312 CORRUPTED?? 416826464 CORRUPTED???? 1698518 > ?------------------------------------------------------------------ > ?[PEAK NUMBER? 116]?????? PEAK MEMORY????? 14169180 =? 113.4 MBytes > ?[ALL. NUMBER? 116]????? TOTAL MEMORY????? 13983696 =? 111.9 MBytes > ?================================================================== > > > ?PROGRAM STOPS IN SUBROUTINE MEMORY_CHECK|? CORRUPTED MEMORY [PROC=?? > 9] > ?[PEAK NUMBER? 116]?????? PEAK MEMORY????? 14169180 =? 113.4 MBytes > ?[ALL. NUMBER? 116]????? TOTAL MEMORY????? 13983696 =? 111.9 MBytes > ?================================================================== > > > ?PROGRAM STOPS IN SUBROUTINE MEMORY_CHECK|? CORRUPTED MEMORY [PROC=? > 10] > PC: 0xb18ca40 MPI_SGI_stacktraceback in /usr/lib64/libmpi.so > PC: 0xb1b5e30 PMPI_Abort in /usr/lib64/libmpi.so > PC: 0xb1e84b8 pmpi_abort_ in /usr/lib64/libmpi.so > PC: 0x10624edc stopgm in > /home/irix/meen/jzhang/qmmm/CPMD-3.11.1/SOURCE/cpmd.x > PC: 0x1049884c memory_check in > /home/irix/meen/jzhang/qmmm/CPMD-3.11.1/SOURCE/cpmd.x > PC: 0x1051866c testex in /home/irix/meen/jzhang/qmmm/CPMD- > 3.11.1/SOURCE/cpmd.x > PC: 0x10447cd4 updwf in > /home/irix/meen/jzhang/qmmm/CPMD-3.11.1/SOURCE/cpmd.x > PC: 0x10399770 interface in > /home/irix/meen/jzhang/qmmm/CPMD-3.11.1/SOURCE/cpmd.x > PC: 0x10633614 interpt in /home/irix/meen/jzhang/qmmm/CPMD- > 3.11.1/SOURCE/cpmd.x > PC: 0x10698438 cpmd in > /home/irix/meen/jzhang/qmmm/CPMD-3.11.1/SOURCE/cpmd.x > PC: 0x10698510 cpmd_stuttgart in > /home/irix/meen/jzhang/qmmm/CPMD-3.11.1/SOURCE/cpmd.x > PC: 0x291fc34 main in /usr/lib64/libftn.so > > > -- > Sincerely yours, > James jianzhang > Department of Mechanical and Chemical Engineering > North Carolina Agricultural and Technical State University > 1601 East Market Street > Greensboro, NC 27411 > ? > > > -- > Sincerely yours, > James jianzhang > Department of Mechanical and Chemical Engineering > North Carolina Agricultural and Technical State University > 1601 East Market Street > Greensboro, NC 27411 > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Pradip K. Biswas, PhD. Research Associate, Department of Chemistry; Cleveland State University, Ohio-44115 Phone: 1-216-875-9723 http://comppsi.csuohio.edu/groups/people/biswas.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 3773 bytes Desc: not available URL: From p.biswas at csuohio.edu Wed Sep 20 17:50:02 2006 From: p.biswas at csuohio.edu (Pradip Kumar Biswas) Date: Wed, 20 Sep 2006 11:50:02 -0400 Subject: [gmx-users] running CPMD with GROMACS interface in SGI irix 6.5 In-Reply-To: <93e2edd90609121810x3631409fy8e44a8a78c346997@mail.gmail.com> References: <93e2edd90609121810x3631409fy8e44a8a78c346997@mail.gmail.com> Message-ID: James, Could you please send me the 'output.mdrun_xx' (xx=em or md) file where this error message is printed? Which CPMD version are you using? Pradip. On Sep 12, 2006, at 9:10 PM, james zhang wrote: > Hi > ? > I got some trouble in running CPMD with GROMACS?interface?in SGI irix > 6.5. Thanks in advance > ? > the error is > > ?[PEAK NUMBER? 116]?????? PEAK MEMORY????? 14169180 =? 113.4 MBytes > ?[ALL. NUMBER? 116]????? TOTAL MEMORY????? 13983696 =? 111.9 MBytes > ?================================================================== > > > ?PROGRAM STOPS IN SUBROUTINE MEMORY_CHECK|? CORRUPTED MEMORY [PROC=?? > 8] > ?EIGV???????? 390897072 CORRUPTED?? 390994624 CORRUPTED?????? 12193 > ?SC0????????? 390994640 CORRUPTED?? 391254032 CORRUPTED?????? 32423 > ?PME????????? 391254048 CORRUPTED?? 391513440 CORRUPTED?????? 32423 > ?GDE????????? 391513456 CORRUPTED?? 391772848 CORRUPTED?????? 32423 > ?HGPOT??????? 391860984 CORRUPTED?? 392180992 CORRUPTED?????? 40000 > ?HIPZ???????? 392181008 CORRUPTED?? 394741016 CORRUPTED????? 320000 > ?NZFFP??????? 394741032 CORRUPTED?? 396297320 CORRUPTED????? 194535 > ?NZFSP??????? 396297336 CORRUPTED?? 396987776 CORRUPTED?????? 86304 > ??? 396987792 CORRUPTED?? 403238296 CORRUPTED????? 781312 > ??? 403238312 CORRUPTED?? 416826464 CORRUPTED???? 1698518 > ?------------------------------------------------------------------ > ?[PEAK NUMBER? 116]?????? PEAK MEMORY????? 14169180 =? 113.4 MBytes > ?[ALL. NUMBER? 116]????? TOTAL MEMORY????? 13983696 =? 111.9 MBytes > ?================================================================== > > > ?PROGRAM STOPS IN SUBROUTINE MEMORY_CHECK|? CORRUPTED MEMORY [PROC=?? > 9] > ?[PEAK NUMBER? 116]?????? PEAK MEMORY????? 14169180 =? 113.4 MBytes > ?[ALL. NUMBER? 116]????? TOTAL MEMORY????? 13983696 =? 111.9 MBytes > ?================================================================== > > > ?PROGRAM STOPS IN SUBROUTINE MEMORY_CHECK|? CORRUPTED MEMORY [PROC=? > 10] > PC: 0xb18ca40 MPI_SGI_stacktraceback in /usr/lib64/libmpi.so > PC: 0xb1b5e30 PMPI_Abort in /usr/lib64/libmpi.so > PC: 0xb1e84b8 pmpi_abort_ in /usr/lib64/libmpi.so > PC: 0x10624edc stopgm in > /home/irix/meen/jzhang/qmmm/CPMD-3.11.1/SOURCE/cpmd.x > PC: 0x1049884c memory_check in > /home/irix/meen/jzhang/qmmm/CPMD-3.11.1/SOURCE/cpmd.x > PC: 0x1051866c testex in /home/irix/meen/jzhang/qmmm/CPMD- > 3.11.1/SOURCE/cpmd.x > PC: 0x10447cd4 updwf in > /home/irix/meen/jzhang/qmmm/CPMD-3.11.1/SOURCE/cpmd.x > PC: 0x10399770 interface in > /home/irix/meen/jzhang/qmmm/CPMD-3.11.1/SOURCE/cpmd.x > PC: 0x10633614 interpt in /home/irix/meen/jzhang/qmmm/CPMD- > 3.11.1/SOURCE/cpmd.x > PC: 0x10698438 cpmd in > /home/irix/meen/jzhang/qmmm/CPMD-3.11.1/SOURCE/cpmd.x > PC: 0x10698510 cpmd_stuttgart in > /home/irix/meen/jzhang/qmmm/CPMD-3.11.1/SOURCE/cpmd.x > PC: 0x291fc34 main in /usr/lib64/libftn.so > > > -- > Sincerely yours, > James jianzhang > Department of Mechanical and Chemical Engineering > North Carolina Agricultural and Technical State University > 1601 East Market Street > Greensboro, NC 27411 > ? > > > -- > Sincerely yours, > James jianzhang > Department of Mechanical and Chemical Engineering > North Carolina Agricultural and Technical State University > 1601 East Market Street > Greensboro, NC 27411 > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Pradip K. Biswas, PhD. Research Associate, Department of Chemistry; Cleveland State University, Ohio-44115 Phone: 1-216-875-9723 http://comppsi.csuohio.edu/groups/people/biswas.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 3760 bytes Desc: not available URL: From sir_donald_bradman at yahoo.com Wed Sep 20 18:12:01 2006 From: sir_donald_bradman at yahoo.com (Manohar Murthi) Date: Wed, 20 Sep 2006 09:12:01 -0700 (PDT) Subject: [gmx-users] Re: umbrella sampling pull.pdo output In-Reply-To: <20060919183531.3150924080@xray.bmc.uu.se> Message-ID: <20060920161202.86848.qmail@web51014.mail.yahoo.com> > > is this perchance a bug or am i doing something > wrong? > sorry, i rtfm. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From Florian.Haberl at chemie.uni-erlangen.de Wed Sep 20 18:38:39 2006 From: Florian.Haberl at chemie.uni-erlangen.de (Florian Haberl) Date: Wed, 20 Sep 2006 18:38:39 +0200 Subject: [gmx-users] Installation of Gromacs into BG/L In-Reply-To: <20060920100340.A822.FUJISAKI@bu.edu> References: <20060920100340.A822.FUJISAKI@bu.edu> Message-ID: <200609201838.40139.Florian.Haberl@chemie.uni-erlangen.de> hi, On Wednesday 20 September 2006 16:07, Hiroshi Fujisaki wrote: > Dear Gromacs users, > > I am now trying to install gromacs into our BlueGene facility, > but I fail when I do make. (configure seems to be fine.) > The link to the FFTW library does not seem to work. > I use fftw-2.1.5. I attach the excerpt of the make log file here > (the last part of the log). Have yout tried it with fftw 3.1.2 version? perhaps some problem with linking to X? so configure --without-x and malloc > > ########################################################################### >######### > > cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -maltivec > -mabi=altivec -mcpu=7450 -mtune=970 -o mdrun glaasje.o gctio.o init_sh.o > ionize.o do_gct.o relax_sh.o repl_ex.o xutils.o md.o mdrun.o genalg.o > -L/bgl/local/fftw-2.1.5/lib ../mdlib/.libs/libmd_d.a -L/usr/X11R6/lib > ../gmxlib/.libs/libgmx_d.a -lnsl /bgl/local/fftw-2.1.5/lib/librfftw.a > /bgl/local/fftw-2.1.5/lib/libfftw.a -lm /usr/X11R6/lib/libXm.so -lXt -lSM > -lICE -lXext -lXp -lX11 > /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x56): In function > `read_int': /u/walkup/download/fftw-2.1.5/fftw/wisdom.c:224: undefined > reference to `__ctype_b' > /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x62):/u/walkup/downloa >d/fftw-2.1.5/fftw/wisdom.c:224: undefined reference to `__ctype_b' > /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x9e):/u/walkup/downloa >d/fftw-2.1.5/fftw/wisdom.c:229: undefined reference to `__ctype_b' > /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0xfa): In function > `eat_blanks': /u/walkup/download/fftw-2.1.5/fftw/wisdom.c:209: undefined > reference to `__ctype_b' > /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x102):/u/walkup/downlo >ad/fftw-2.1.5/fftw/wisdom.c:209: undefined reference to `__ctype_b' > /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x126):/u/walkup/downlo >ad/fftw-2.1.5/fftw/wisdom.c:209: more undefined references to `__ctype_b' > follow /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x26a): In > function `toupper': > /bgl/BlueLight/ppcfloor/blrts-gnu/powerpc-bgl-blrts-gnu/sys-include/ctype.h >:176: undefined reference to `__ctype_toupper' > /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x276):/bgl/BlueLight/p >pcfloor/blrts-gnu/powerpc-bgl-blrts-gnu/sys-include/ctype.h:176: undefined > reference to `__ctype_toupper' > /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x28e): In function > `tolower': > /bgl/BlueLight/ppcfloor/blrts-gnu/powerpc-bgl-blrts-gnu/sys-include/ctype.h >:170: undefined reference to `__ctype_tolower' > /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x29a):/bgl/BlueLight/p >pcfloor/blrts-gnu/powerpc-bgl-blrts-gnu/sys-include/ctype.h:170: undefined > reference to `__ctype_tolower' > /bgl/local/fftw-2.1.5/lib/libfftw.a(rader.o)(.text+0x128): In function > `fftwi_twiddle_rader': /u/walkup/download/fftw-2.1.5/fftw/rader.c:273: > undefined reference to `__divi64' > /bgl/local/fftw-2.1.5/lib/libfftw.a(rader.o)(.text+0x244):/u/walkup/downloa >d/fftw-2.1.5/fftw/rader.c:321: undefined reference to `__divi64' > /bgl/local/fftw-2.1.5/lib/libfftw.a(rader.o)(.text+0x470): In function > `fftw_twiddle_rader': /u/walkup/download/fftw-2.1.5/fftw/rader.c:190: > undefined reference to `__divi64' > /bgl/local/fftw-2.1.5/lib/libfftw.a(rader.o)(.text+0x590):/u/walkup/downloa >d/fftw-2.1.5/fftw/rader.c:238: undefined reference to `__divi64' > /bgl/local/fftw-2.1.5/lib/libfftw.a(rader.o)(.text+0x8ac): In function > `create_rader_aux': /u/walkup/download/fftw-2.1.5/fftw/rader.c:115: > undefined reference to `__divi64' > /bgl/local/fftw-2.1.5/lib/libfftw.a(rader.o)(.text+0xa7c):/u/walkup/downloa >d/fftw-2.1.5/fftw/rader.c:59: more undefined references to `__divi64' follow > collect2: ld returned 1 exit status > make[3]: *** [mdrun] Error 1 > make[3]: Leaving directory > `/project2/gaussden/fujisaki/src/gromacs-3.3.1/src/kernel' make[2]: *** > [all-recursive] Error 1 > make[2]: Leaving directory > `/project2/gaussden/fujisaki/src/gromacs-3.3.1/src' make[1]: *** [all] > Error 2 > make[1]: Leaving directory > `/project2/gaussden/fujisaki/src/gromacs-3.3.1/src' make: *** > [all-recursive] Error 1 > > ########################################################################### >############# > > I appreciate your help. > > Best wishes, Greetings, Florian -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) ? 9131 ? 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- From thompsma at jilau1.colorado.edu Wed Sep 20 20:59:22 2006 From: thompsma at jilau1.colorado.edu (Matt Thompson) Date: Wed, 20 Sep 2006 12:59:22 -0600 Subject: [gmx-users] Water Tutorial and g_rdf Message-ID: <45118F8A.9030503@jilau1.colorado.edu> Folks, I'm a newbie at GROMACS who is going through the tutorial outlined here: http://www.gromacs.org/documentation/reference_3.3/online/water.html All is well (aside from the bd-temp warning at the grompp command) until I try to analyze the system. Namely when I run: g_rdf -n index it seems to lockup. Now, maybe it's supposed to take a while, I don't know, but after 35 minutes of 100% CPU on a Pentium D (and no end in sight), I began to wonder. When I run it, the output on screen is: > g_rdf -n index :-) G R O M A C S (-: GRowing Old MAkes el Chrono Sweat :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) g_rdf (-: ***CUT THE OPTIONS*** Select a reference group and 1 group Group 0 ( OW) has 216 elements There is one group in the index There is one group in the index Reading frame 0 time 0.000 After that point, it takes a proc and runs with it. Now one thing I noticed was that in the tutorial it says: The program will ask you for how many groups you want the calculate the RDF, answer 1 The program doesn't ask me. FYI, I compiled the program using the gromacs-3.3-1.src.rpm spec file but altered to use the 3.3.1 sources. I have the compilation log that I tee'd, but the lines involving g_rdf don't have any error attached. Thank you for any help, Matt Thompson -- The mayfly lives only one day, and sometimes it rains. - Geo. Carlin Matt Thompson -- http://ucsub.colorado.edu/~thompsma/ 440 UCB, Boulder, CO 80309-0440 JILA A510, 303-492-4662 From fujisaki at bu.edu Wed Sep 20 22:16:12 2006 From: fujisaki at bu.edu (Hiroshi Fujisaki) Date: Wed, 20 Sep 2006 16:16:12 -0400 Subject: [gmx-users] Installation of Gromacs into BG/L In-Reply-To: <200609201838.40139.Florian.Haberl@chemie.uni-erlangen.de> References: <20060920100340.A822.FUJISAKI@bu.edu> <200609201838.40139.Florian.Haberl@chemie.uni-erlangen.de> Message-ID: <20060920161446.7D86.FUJISAKI@bu.edu> Dear Florian, Thanks for your help. It worked! I should have tried fftw-3.1.2 first ... Best wishes, > hi, > > On Wednesday 20 September 2006 16:07, Hiroshi Fujisaki wrote: > > Dear Gromacs users, > > > > I am now trying to install gromacs into our BlueGene facility, > > but I fail when I do make. (configure seems to be fine.) > > The link to the FFTW library does not seem to work. > > I use fftw-2.1.5. I attach the excerpt of the make log file here > > (the last part of the log). > > Have yout tried it with fftw 3.1.2 version? > perhaps some problem with linking to X? > > so configure --without-x and malloc > > > > > ########################################################################### > >######### > > > > cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -maltivec > > -mabi=altivec -mcpu=7450 -mtune=970 -o mdrun glaasje.o gctio.o init_sh.o > > ionize.o do_gct.o relax_sh.o repl_ex.o xutils.o md.o mdrun.o genalg.o > > -L/bgl/local/fftw-2.1.5/lib ../mdlib/.libs/libmd_d.a -L/usr/X11R6/lib > > ../gmxlib/.libs/libgmx_d.a -lnsl /bgl/local/fftw-2.1.5/lib/librfftw.a > > /bgl/local/fftw-2.1.5/lib/libfftw.a -lm /usr/X11R6/lib/libXm.so -lXt -lSM > > -lICE -lXext -lXp -lX11 > > /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x56): In function > > `read_int': /u/walkup/download/fftw-2.1.5/fftw/wisdom.c:224: undefined > > reference to `__ctype_b' > > /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x62):/u/walkup/downloa > >d/fftw-2.1.5/fftw/wisdom.c:224: undefined reference to `__ctype_b' > > /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x9e):/u/walkup/downloa > >d/fftw-2.1.5/fftw/wisdom.c:229: undefined reference to `__ctype_b' > > /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0xfa): In function > > `eat_blanks': /u/walkup/download/fftw-2.1.5/fftw/wisdom.c:209: undefined > > reference to `__ctype_b' > > /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x102):/u/walkup/downlo > >ad/fftw-2.1.5/fftw/wisdom.c:209: undefined reference to `__ctype_b' > > /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x126):/u/walkup/downlo > >ad/fftw-2.1.5/fftw/wisdom.c:209: more undefined references to `__ctype_b' > > follow /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x26a): In > > function `toupper': > > /bgl/BlueLight/ppcfloor/blrts-gnu/powerpc-bgl-blrts-gnu/sys-include/ctype.h > >:176: undefined reference to `__ctype_toupper' > > /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x276):/bgl/BlueLight/p > >pcfloor/blrts-gnu/powerpc-bgl-blrts-gnu/sys-include/ctype.h:176: undefined > > reference to `__ctype_toupper' > > /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x28e): In function > > `tolower': > > /bgl/BlueLight/ppcfloor/blrts-gnu/powerpc-bgl-blrts-gnu/sys-include/ctype.h > >:170: undefined reference to `__ctype_tolower' > > /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x29a):/bgl/BlueLight/p > >pcfloor/blrts-gnu/powerpc-bgl-blrts-gnu/sys-include/ctype.h:170: undefined > > reference to `__ctype_tolower' > > /bgl/local/fftw-2.1.5/lib/libfftw.a(rader.o)(.text+0x128): In function > > `fftwi_twiddle_rader': /u/walkup/download/fftw-2.1.5/fftw/rader.c:273: > > undefined reference to `__divi64' > > /bgl/local/fftw-2.1.5/lib/libfftw.a(rader.o)(.text+0x244):/u/walkup/downloa > >d/fftw-2.1.5/fftw/rader.c:321: undefined reference to `__divi64' > > /bgl/local/fftw-2.1.5/lib/libfftw.a(rader.o)(.text+0x470): In function > > `fftw_twiddle_rader': /u/walkup/download/fftw-2.1.5/fftw/rader.c:190: > > undefined reference to `__divi64' > > /bgl/local/fftw-2.1.5/lib/libfftw.a(rader.o)(.text+0x590):/u/walkup/downloa > >d/fftw-2.1.5/fftw/rader.c:238: undefined reference to `__divi64' > > /bgl/local/fftw-2.1.5/lib/libfftw.a(rader.o)(.text+0x8ac): In function > > `create_rader_aux': /u/walkup/download/fftw-2.1.5/fftw/rader.c:115: > > undefined reference to `__divi64' > > /bgl/local/fftw-2.1.5/lib/libfftw.a(rader.o)(.text+0xa7c):/u/walkup/downloa > >d/fftw-2.1.5/fftw/rader.c:59: more undefined references to `__divi64' follow > > collect2: ld returned 1 exit status > > make[3]: *** [mdrun] Error 1 > > make[3]: Leaving directory > > `/project2/gaussden/fujisaki/src/gromacs-3.3.1/src/kernel' make[2]: *** > > [all-recursive] Error 1 > > make[2]: Leaving directory > > `/project2/gaussden/fujisaki/src/gromacs-3.3.1/src' make[1]: *** [all] > > Error 2 > > make[1]: Leaving directory > > `/project2/gaussden/fujisaki/src/gromacs-3.3.1/src' make: *** > > [all-recursive] Error 1 > > > > ########################################################################### > >############# > > > > I appreciate your help. > > > > Best wishes, > > Greetings, > > Florian > -- > ------------------------------------------------------------------------------- > Florian Haberl > Computer-Chemie-Centrum > Universitaet Erlangen/ Nuernberg > Naegelsbachstr 25 > D-91052 Erlangen > Telephone: +49(0) $BchC(B9131 $BchC(B85 26581 > Mailto: florian.haberl AT chemie.uni-erlangen.de > ------------------------------------------------------------------------------- > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Hiroshi Fujisaki From chris.neale at utoronto.ca Wed Sep 20 22:35:06 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Wed, 20 Sep 2006 16:35:06 -0400 Subject: [gmx-users] 1-4 columb interaction Message-ID: <20060920163506.kpdlw6ck8mww4coc@webmail.utoronto.ca> You are right that the LJ fudge values don't get applied if gen-pairs=no. However, FudgeQQ is always applied. However, one would hope that Qiao was correct and the main .itp files at least list the correct scaling of LJ 1-4 interactions. Force fields that use gen-pairs=no explicitly list 1-4 LJ parameters in the pairtypes section. This appears to be the case in the gromos96 force field. For example, [ nonbond_params ] ; i j func c6 c12 OM O 1 0.0022619536 7.4149321e-07 [ pairtypes ] ; i j func c6 c12 OM O 1 0.0022619536 7.4149321e-07 So a 1-4 (pairtypes) and a 1->5 or nonbonded LJ are going to be the same. The treatment of 1-4 interactions is quite well described in the gromacs manual. ----- Original Message ----- Thanks Qiao for your reply. But If I am using genpair = no (GROMOS 96 force field) then there is no meaning of fudgeLJ and fudgeQQ (correct me if I am wrong). So more specific if I am using GROMOS96 force field then is there any scaling for 1-4 columb interaction?? if yes then how? From akshay17 at olemiss.edu Wed Sep 20 23:51:17 2006 From: akshay17 at olemiss.edu (Akshay Patny) Date: Wed, 20 Sep 2006 16:51:17 -0500 Subject: [gmx-users] Which POPC Bilayer to start? Message-ID: <000e01c6dcfe$e6779b80$8aa74a82@Plasma> Hi All I am trying to use POPC bilayer for doing GPCR simulation. I have come across two options of generating a POPC bilayer >>>> 1. I can generate a POPC bilayer from the VMD Membrane plug-in, wherein the membrane is generated from the pre-built membrane square patches and lipid tails are (almost) fully extended. 2. Alternatively, I can download the pre-equilibrated POPC bilayer from Dr. Tieleman's website, http://moose.bio.ucalgary.ca/index.php?page=People Since, I am new to the GPCR-membrane modeling, can you suggest me which out of the above two options can be a better starting point for the simulation of my GPCR protein? A membrane generated from VMD or a pre-equilibrated membrane?? Would the equilibration time for my protein be lesser in one out of the two? If option 2 is a good idea then out of popc128a.pdb and popc128b.pdb (both available from Prof. Tieleman's website), which will be a better model to start with? Thank you very much in advance. Akshay Akshay Patny Graduate Research Assistant Faser Hall 417, Department of Medicinal Chemistry Research Institute of Pharmaceutical Sciences University of Mississippi University, MS 38677 E-mail: akshay17 at olemiss.edu Tel: 662-915-1286 (office); Web: www.olemiss.edu From fujisaki at bu.edu Thu Sep 21 02:08:29 2006 From: fujisaki at bu.edu (Hiroshi Fujisaki) Date: Wed, 20 Sep 2006 20:08:29 -0400 Subject: [gmx-users] execution of water tutorial files on BG/L Message-ID: <20060920200039.7D95.FUJISAKI@bu.edu> Dear Gromacs users, After installing fftw-3.1.2 and gromacs itself on our BlueGene facility, I am testing the tutorial files, but I fail when I try all of them. For example, for the water case (.../share/gromacs/tutor/water), "grompp -v" seems to work, but "mdrun -v" suddenly stops with the following message "Illegal instruction" I've never experienced this when I use gromacs in a linux machine. Could you suggest something? The gromacs was compiled with a single precision and single CPU version. I appreciate your help. Best wishes, -- Hiroshi Fujisaki From Dallas.Warren at vcp.monash.edu.au Thu Sep 21 02:09:46 2006 From: Dallas.Warren at vcp.monash.edu.au (Dallas B. Warren) Date: Thu, 21 Sep 2006 10:09:46 +1000 Subject: [gmx-users] question about energy and pressure In-Reply-To: <6a91f07b0609200513g5c404d49gd5e5e8f784afd0b6@mail.gmail.com> Message-ID: <89907EA1DCFB7548A431C13A270F9DD502380911@prk-exch-01.vcp.local> >1. I simualted a pure small molecule system. All the simulation is ok. But >when I use g_energy to calculate the energy of bond, angle, lj, and coloumb, >it gives the following energy. The energies is much bigger, about 50-100 times >bigger than the reported data. What's wrong? Well, that depends on what the reported data actually is to whether you can actually make the comparison. Is it for exactly the same system with the same forcefield? Is it for the entire system or for per molecule? Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.warren at vcp.monash.edu.au +61 3 9903 9524 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From vechism at netscape.net Thu Sep 21 02:34:56 2006 From: vechism at netscape.net (vechism at netscape.net) Date: Wed, 20 Sep 2006 20:34:56 -0400 Subject: [gmx-users] EM problem with OPLS and TIP4P Message-ID: <8C8AB2CE59AC3BD-16B4-17F4@FWM-M35.sysops.aol.com> Dear Gromacs users, I am trying to run a MD simulation of a protein using OPLS and TIP4P in the same way as I already did before using GROMOS and SPC water but when I run the mdrun for the Energy Minimization I get the error described below. These errors occur during the EM (the mdp file is enclosed): (a) using only one processor: Step 20, Epot=-1.117652e+07, Fnorm=2.168e+03, Fmax=6.133e+03 (atom 12802) Step 21, Epot=-1.188519e+07, Fnorm=2.613e+03, Fmax=1.336e+04 (atom 3990) Step 22, Epot=-1.193758e+07, Fnorm=2.724e+03, Fmax=1.581e+04 (atom 3990) Step 23, Epot=-1.492766e+07, Fnorm=2.250e+04, Fmax=2.177e+06 (atom 3990) Step 24, Epot=-1.276652e+22, Fnorm= inf, Fmax= inf (atom 86) In this case, the program do not display any error messages, just stay running but do not return anything else. (b) using two processors: Step 20, Epot=-1.117643e+07, Fnorm=2.168e+03, Fmax=6.133e+03 (atom 1) Step 21, Epot=-1.188507e+07, Fnorm=2.613e+03, Fmax=1.336e+04 (atom 3990) Step 22, Epot=-1.193749e+07, Fnorm=2.724e+03, Fmax=1.581e+04 (atom 3990) Step 23, Epot=-1.492768e+07, Fnorm=2.250e+04, Fmax=2.177e+06 (atom 3990) Step 24, Epot= nan, Fnorm= nan, Fmax= inf (atom 36) Fatal error: ci = -2147483648 should be in 0 .. 511 [FILE nsgrid.c, LINE 218] Fatal error: ci = -2147483648 should be in 0 .. 511 [FILE nsgrid.c, LINE 218] ----------------------------------------------------------------------------- One of the processes started by mpirun has exited with a nonzero exit code. This typically indicates that the process finished in error. If your process did not finish in error, be sure to include a "return 0" or "exit(0)" in your C code before exiting the application. PID 7295 failed on node n0 (127.0.0.1) with exit status 32767. ----------------------------------------------------------------------------- (c) using 1 processor and a bigger simulation box: Step 20, Epot=-1.632885e+07, Fnorm=2.296e+03, Fmax=6.372e+03 (atom 32295) Step 21, Epot=-1.716738e+07, Fnorm=2.151e+03, Fmax=6.880e+03 (atom 10791) Step 22, Epot=-1.966934e+07, Fnorm=7.181e+03, Fmax=8.281e+04 (atom 22371) Step 23, Epot=-1.973746e+07, Fnorm=7.382e+03, Fmax=1.002e+05 (atom 22371) Step 24, Epot= nan, Fnorm= nan, Fmax=2.685e+06 (atom 4546) Fatal error: ci = -2147483648 should be in 0 .. 728 [FILE nsgrid.c, LINE 218] ------------------------------------------------------------------------------------- A piece of my mdp file: ******************************************************************** ; cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = cg ;integrator = steep nsteps = 100000 unconstrained_start = yes nstxout = 100 nstvout = 100 nstfout = 100 nstlog = 100 nstenergy = 100 ; ; ENERGY MINIMIZATION OPTIONS ; ; Force tolerance and initial step-size emtol = 100 emstep = 0.0001 ; ; Frequency of steepest descents steps when doing Conjugated Gradient nstcgsteep = 10 ************************************************************************ The atoms: 86 in (a), 36 in (b) and 4546 in (c) are hydrogen atoms. I have read the mailing list and whereas I found some similar errors I haven't found the answer yet. Could someone help me with some clues? Thanks in advance, Sergio ________________________________________________________________________ Check Out the new free AIM(R) Mail -- 2 GB of storage and industry-leading spam and email virus protection. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chris.neale at utoronto.ca Thu Sep 21 03:28:23 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Wed, 20 Sep 2006 21:28:23 -0400 Subject: [gmx-users] EM problem with OPLS and TIP4P Message-ID: <20060920212823.nln50eq0gr48c4kg@webmail.utoronto.ca> Try this: unconstrained_start = no Also ensure that your .top file is correct. Also take a look at your starting positions, where is MW? Also ensure that your waters have the correct order: eg. 871SOL OW 3496 1.935 2.093 1.901 871SOL HW1 3497 1.902 2.172 1.945 871SOL HW2 3498 1.990 2.126 1.830 871SOL MW 3499 1.938 2.107 1.898 Also try outputting coords for step 20,21,22,23 in the first system and see what is actually happening. From chris.neale at utoronto.ca Thu Sep 21 03:31:56 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Wed, 20 Sep 2006 21:31:56 -0400 Subject: [gmx-users] single and double Message-ID: <20060920213156.nla56vb6fz4gkowc@webmail.utoronto.ca> Thank you very much St?phane, that's great info. ---original message--- chris.neale at utoronto.ca a ?crit : > My system here is an opls-aa protein in a POPE/DMPE membrane with > tip4p waters. > > Prior to adding counterions, grompp yields a net charge of -1.999973 > and grompp_d yields -2.0. Once I have added counterions, both single > and double precision don't give me a warning about a net charge on > the system. Either system runs fine for many ns and they don't crash. > > 1. Is the net charge really as close to 0.0 in the single precision > version as it is in the double, or just close enough that there is > no warning issued? The net charge is really close to zero, the difference may rely on hardware roundoff, and on the topology limits (charge precision on each atom/group). This is why you see the difference between single and double precision. > 2. If single is farther from 0.0, is this a problem? It depends :-) I assume you're using PME, in this case, the system will be scaled to 0 and for you run, that won't be a problem (since spreading a <1e-4 charges among >100 000 atoms won't interfere much with their net charge ...) and the roundoff errors due to the calculations themselves are bigger than this single vs double difference. > 3. Why does single run faster anyway? I though intel processors > treated them the exact same way in terms of the operations that > needed to be carried out? It depends of the hardware you're talking about. On single precision systems, the run would run at the same speed on 32 bits architecture and on 64 bits architectures. On double precision systems, the same run will take twice the time on 32 bits than on 64bits (roughly). Globally, single precision == 32bits, double precision == 64bits. That means on single precision run on 32bits machines will be done in the same time that double precision on 64bits (roughly again). This is more or less true with gromacs since processors have more than two types of calculation units (thinkk of sse, sse2, 3Dnowext, ...) and gromacs is able to take most of them (if not all) into account via specialized routines, but that the goal. > Thanks. > Chris. Cheers, St?phane From qiaobf at gmail.com Thu Sep 21 09:14:08 2006 From: qiaobf at gmail.com (Qiao Baofu) Date: Thu, 21 Sep 2006 09:14:08 +0200 Subject: [gmx-users] question about energy and pressure In-Reply-To: <89907EA1DCFB7548A431C13A270F9DD502380911@prk-exch-01.vcp.local> References: <6a91f07b0609200513g5c404d49gd5e5e8f784afd0b6@mail.gmail.com> <89907EA1DCFB7548A431C13A270F9DD502380911@prk-exch-01.vcp.local> Message-ID: <6a91f07b0609210014n2ca18590uc08cd80e5b92a0dd@mail.gmail.com> Hi Dallas Warren, 1. The molecules are the same. But we built the system in different method, and used different number of molecules. 2. We both used the oplsaa all-atom force field, but the parameters are a little different. 3. I used gromacs. The reference used MDynaMix. 4. The unit of energy are both KJ/mol I think no matter what softwares or systems, the energies should almost the same. At least, they should not deviate to much? is it right? PS: For the pressure, I used Berendsen pressure coupling. 2006/9/21, Dallas B. Warren : > > >1. I simualted a pure small molecule system. All the simulation is ok. > But > >when I use g_energy to calculate the energy of bond, angle, lj, and > coloumb, > >it gives the following energy. The energies is much bigger, about > 50-100 times > >bigger than the reported data. What's wrong? > > Well, that depends on what the reported data actually is to whether you > can actually make the comparison. > > Is it for exactly the same system with the same forcefield? > > Is it for the entire system or for per molecule? > > Catch ya, > > Dr. Dallas Warren > Lecturer > Department of Pharmaceutical Biology and Pharmacology > Victorian College of Pharmacy, Monash University > 381 Royal Parade, Parkville VIC 3010 > dallas.warren at vcp.monash.edu.au > +61 3 9903 9524 > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble > a nail. > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Sincerely yours, ********************************************** Baofu Qiao, PhD Frankfurt Institute for Advanced Studies Max-von-Laue-Str. 1 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From nunolf at ci.uc.pt Thu Sep 21 11:39:08 2006 From: nunolf at ci.uc.pt (Nuno Ricardo Loureiro Ferreira) Date: Thu, 21 Sep 2006 10:39:08 +0100 Subject: [gmx-users] Recover corrupted files from DVD Message-ID: <000a01c6dd61$cb175cf0$150110ac@gandalf> Hi * I burned several DVD's during a project (and deleted the original files after having verified the saved data, no disk space ;-), and today I just realized that I'm having problems getting the data from one of them, and unfortunely corresponds more or less to the middle of a certain trajectory. Do you guys think that running again that missing part of the traj from the last saved .trr, will give me the same results? It was run on a box that I no longer have access. Do the trajs done in different boxes give different (or slightly different) trajs using the same gmx version? BTW, do you recommend any soft that I can use to try to try to recover files froma CD/DVD (iso9600)? Best regards, Nuno -------------- next part -------------- An HTML attachment was scrubbed... URL: From erikm at xray.bmc.uu.se Thu Sep 21 13:06:28 2006 From: erikm at xray.bmc.uu.se (Erik Marklund) Date: Thu, 21 Sep 2006 13:06:28 +0200 Subject: [gmx-users] Recover corrupted files from DVD In-Reply-To: <000a01c6dd61$cb175cf0$150110ac@gandalf> References: <000a01c6dd61$cb175cf0$150110ac@gandalf> Message-ID: <1158836789.27779.6.camel@jorn.bmc.uu.se> On Thu, 2006-09-21 at 10:39 +0100, Nuno Ricardo Loureiro Ferreira wrote: > Hi * > > I burned several DVD's during a project (and deleted the original > files after having verified the saved data, no disk space ;-), and > today I just realized that I'm having problems getting the data from > one of them, and unfortunely corresponds more or less to the middle of > a certain trajectory. > > Do you guys think that running again that missing part of the traj > from the last saved .trr, will give me the same results? > It was run on a box that I no longer have access. Do the trajs done in > different boxes give different (or slightly different) trajs using the > same gmx version? Sorry, but different computers may introduce different numerical error, producing different trajectories. I would not recommend it. Of course, you could try and see whether the last frames of the "patch" trajectory are identical to the corresponding frames of the old broken trajectory, but I wouldn't bet on it. /Erik > > BTW, do you recommend any soft that I can use to try to try to recover > files froma CD/DVD (iso9600)? > > Best regards, > Nuno > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Erik Marklund, PhD Student, Molecular Biopcysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 erikm at xray.bmc.uu.se From spitaleri.andrea at hsr.it Thu Sep 21 13:29:01 2006 From: spitaleri.andrea at hsr.it (andrea spitaleri) Date: Thu, 21 Sep 2006 13:29:01 +0200 Subject: [gmx-users] Recover corrupted files from DVD In-Reply-To: <1158836789.27779.6.camel@jorn.bmc.uu.se> References: <000a01c6dd61$cb175cf0$150110ac@gandalf> <1158836789.27779.6.camel@jorn.bmc.uu.se> Message-ID: <4512777D.3010709@hsr.it> Hi, anyway a suggestion: run always md5um on the trr files before/after the burn ... you never know andrea Erik Marklund wrote: > On Thu, 2006-09-21 at 10:39 +0100, Nuno Ricardo Loureiro Ferreira wrote: >> Hi * >> >> I burned several DVD's during a project (and deleted the original >> files after having verified the saved data, no disk space ;-), and >> today I just realized that I'm having problems getting the data from >> one of them, and unfortunely corresponds more or less to the middle of >> a certain trajectory. >> >> Do you guys think that running again that missing part of the traj >> from the last saved .trr, will give me the same results? >> It was run on a box that I no longer have access. Do the trajs done in >> different boxes give different (or slightly different) trajs using the >> same gmx version? > > Sorry, but different computers may introduce different numerical error, > producing different trajectories. I would not recommend it. Of course, > you could try and see whether the last frames of the "patch" trajectory > are identical to the corresponding frames of the old broken trajectory, > but I wouldn't bet on it. > > /Erik > >> >> BTW, do you recommend any soft that I can use to try to try to recover >> files froma CD/DVD (iso9600)? >> >> Best regards, >> Nuno >> _______________________________________________ >> gmx-users mailing list gmx-users at gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-request at gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ------------------------------- Andrea Spitaleri Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ ------------------------------- From chris.neale at utoronto.ca Thu Sep 21 15:38:08 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Thu, 21 Sep 2006 09:38:08 -0400 Subject: [gmx-users] 1-4 columb interaction Message-ID: <20060921093808.rxtkbuehnmf4ww44@webmail.utoronto.ca> Quoting Alok : > Thanks Chris for your explanation.and I am sorry to bother you by > writing a personal mail. > > So its mean if I am using default values for genpair (=no), > FudgeLJ(=1.0) and FudgeQQ (=1.0), then I am doing scaling for LJ 14 > interaction only by using separates set of parameters, but not for > 1-4 columb interaction, because I am using FudgeQQ =1.0.And in > GROMOS96 and in ffgmx force field there is not separate set of > parameters for Columb14 interaction. am I correct?? Basically correct. However, there is never a second set of parameters for coulombic 1-4 interactions--it simply is not possible with gromacs-3.3.1, this is the central point that lead to the need for Tieleman's 2006 paper that is mentioned below. > Apart from that in one of your previous mail in gromacs mailing list > .subject : - OPLS and Berger lipid et al Tieleman 2006 > http://www.gromacs.org/pipermail/gmx-users/2006-August/023587.html > > you had mentioned > "However, this 2006 paper appears to be entirely different. If I > understand correctly, the main difference is that they "decided to > replace the 1-4 interactions in the lipids (both the electrostatic > and the Lennard-Jones components) with dihedral potentials.)" > because of the inability to scale columbic separately in Gromacs." > > So if we use FudgeQQ =0.5 there then what is the problem to direct > addition of berger lipid in OPLS force field?? because FudgeQQ is > going to apply on all the cases dosen't matter what we are using > genpair = yes or no.Why they have to replace the 1-4 interaction > with dihedral potential (RB). > The problem is that the FudgeQQ for the Berger lipids should be 1.0 and for OPLS-AA it should be 0.5. There is no way to do this analogously to the LJ parameters that can be set in [ pairs ] or [ pairtypes ]. If you want to base your work on something that has been entirely tested and published, then I suggest that you either live with the 0.5 FudgeQQ scaling for all, or request the new dihedrals from Tieleman's lab (although I believe that they are not yet being made available). If you can accept working with an idea that sounds rigorous but has not yet been tested for more than 5ns or published at all, look here for the method that I use: http://www.gromacs.org/pipermail/gmx-users/2006-September/023761.html and here for Berks much improved suggestion about clean implementaion: http://www.gromacs.org/pipermail/gmx-users/2006-September/023782.html (I am sure the set of zeroes in "with additional 0 0 parameters for the LJ" read sigma epsilon in some font.) > eagry waiting for your reply, > Alok > > ----- Original Message ----- > From: > To: > Sent: Thursday, September 21, 2006 2:05 AM > Subject: [gmx-users] 1-4 columb interaction > > > You are right that the LJ fudge values don't get applied if > gen-pairs=no. However, FudgeQQ is always applied. However, one would > hope that Qiao was correct and the main .itp files at least list the > correct scaling of LJ 1-4 interactions. Force fields that use > gen-pairs=no explicitly list 1-4 LJ parameters in the pairtypes > section. This appears to be the case in the gromos96 force field. For > example, > > [ nonbond_params ] > ; i j func c6 c12 > OM O 1 0.0022619536 7.4149321e-07 > [ pairtypes ] > ; i j func c6 c12 > OM O 1 0.0022619536 7.4149321e-07 > > So a 1-4 (pairtypes) and a 1->5 or nonbonded LJ are going to be the same. > > The treatment of 1-4 interactions is quite well described in the > gromacs manual. > > > ----- Original Message ----- > Thanks Qiao for your reply. > > But If I am using genpair = no (GROMOS 96 force field) then there is > no meaning of fudgeLJ and fudgeQQ (correct me if I am wrong). > > So more specific if I am using GROMOS96 force field then is there any > scaling for 1-4 columb interaction?? > if yes then how? > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > From nunolf at ci.uc.pt Thu Sep 21 15:35:30 2006 From: nunolf at ci.uc.pt (Nuno Ricardo Loureiro Ferreira) Date: Thu, 21 Sep 2006 14:35:30 +0100 Subject: [gmx-users] Recover corrupted files from DVD References: <000a01c6dd61$cb175cf0$150110ac@gandalf><1158836789.27779.6.camel@jorn.bmc.uu.se> <4512777D.3010709@hsr.it> Message-ID: <005201c6dd82$d0542420$150110ac@gandalf> Hi I always do a check sum. It's a rule of thumb here. Erik, your answer was in fact what I was expecting. Thank you. N. ----- Original Message ----- From: "andrea spitaleri" To: "Discussion list for GROMACS users" Sent: Thursday, September 21, 2006 12:29 PM Subject: Re: [gmx-users] Recover corrupted files from DVD > Hi, > anyway a suggestion: run always md5um on the trr files before/after the burn ... > > you never know > > andrea > > Erik Marklund wrote: > > On Thu, 2006-09-21 at 10:39 +0100, Nuno Ricardo Loureiro Ferreira wrote: > >> Hi * > >> > >> I burned several DVD's during a project (and deleted the original > >> files after having verified the saved data, no disk space ;-), and > >> today I just realized that I'm having problems getting the data from > >> one of them, and unfortunely corresponds more or less to the middle of > >> a certain trajectory. > >> > >> Do you guys think that running again that missing part of the traj > >> from the last saved .trr, will give me the same results? > >> It was run on a box that I no longer have access. Do the trajs done in > >> different boxes give different (or slightly different) trajs using the > >> same gmx version? > > > > Sorry, but different computers may introduce different numerical error, > > producing different trajectories. I would not recommend it. Of course, > > you could try and see whether the last frames of the "patch" trajectory > > are identical to the corresponding frames of the old broken trajectory, > > but I wouldn't bet on it. > > > > /Erik > > > >> > >> BTW, do you recommend any soft that I can use to try to try to recover > >> files froma CD/DVD (iso9600)? > >> > >> Best regards, > >> Nuno > >> _______________________________________________ > >> gmx-users mailing list gmx-users at gromacs.org > >> http://www.gromacs.org/mailman/listinfo/gmx-users > >> Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to gmx-users-request at gromacs.org. > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > ------------------------------- > Andrea Spitaleri > Dulbecco Telethon Institute > c/o DIBIT Scientific Institute > Biomolecular NMR, 1B4 > Via Olgettina 58 > 20132 Milano (Italy) > http://biomolecularnmr.ihsr.dom/ > ------------------------------- > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > From steletch at jouy.inra.fr Thu Sep 21 16:11:33 2006 From: steletch at jouy.inra.fr (=?ISO-8859-1?Q?St=E9phane_T=E9letch=E9a?=) Date: Thu, 21 Sep 2006 16:11:33 +0200 Subject: [gmx-users] Recover corrupted files from DVD In-Reply-To: <000a01c6dd61$cb175cf0$150110ac@gandalf> References: <000a01c6dd61$cb175cf0$150110ac@gandalf> Message-ID: <45129D95.3020609@jouy.inra.fr> Nuno Ricardo Loureiro Ferreira a ?crit : > Hi * > > I burned several DVD's during a project (and deleted the original files > after having verified the saved data, no disk space ;-), and today I > just realized that I'm having problems getting the data from one of > them, and unfortunely corresponds more or less to the middle of a > certain trajectory. To really do a backup, you'll need to follow those rules: 1 - two different places (think about fire or water) 2 - tow different media types (hard drive and removable media like CD/DVD, USB key, ...) 3 - do it on a regular basis > Do you guys think that running again that missing part of the traj from > the last saved .trr, will give me the same results? > It was run on a box that I no longer have access. Do the trajs done in > different boxes give different (or slightly different) trajs using the > same gmx version? If you find another computer with the same architecture, you may do it (for instance if you did it on a mono-processor AMD/Intel, it should work, assuming you're getting the same random seed). If the job was done using multi processors (2 or more), you're dead, cpu roundoff, network errors lead to some differences. > BTW, do you recommend any soft that I can use to try to try to recover > files froma CD/DVD (iso9600)? You can try dd: dd if=/dev/hdc of=importantdata.iso Mount the resulting file: mount -o loop importantdata.iso /mnt/iso And try to visualize/repair the files appearing under /mnt/iso (trajconv may help ?). By chance it is possible that only some frames only are missing or corrupted, and you should be able te recover most of the rest (and reconcatenate them). > Best regards, > Nuno I hope it'll help you, Cheers, St?phane -- St?phane T?letch?a, PhD. http://www.steletch.org Unit? Math?matique Informatique et G?nome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert T?l : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901 From alokjain at iitk.ac.in Thu Sep 21 18:22:11 2006 From: alokjain at iitk.ac.in (Alok) Date: Thu, 21 Sep 2006 21:52:11 +0530 Subject: [gmx-users] 1-4 columb interaction References: <20060921093808.rxtkbuehnmf4ww44@webmail.utoronto.ca> Message-ID: <001801c6dd9a$17ca16e0$65741aac@alok> Thanks Chris for your detail reply..... It really help me a lot. Regards, Alok ----- Original Message ----- From: To: Sent: Thursday, September 21, 2006 7:08 PM Subject: [gmx-users] 1-4 columb interaction Quoting Alok : > Thanks Chris for your explanation.and I am sorry to bother you by > writing a personal mail. > > So its mean if I am using default values for genpair (=no), > FudgeLJ(=1.0) and FudgeQQ (=1.0), then I am doing scaling for LJ 14 > interaction only by using separates set of parameters, but not for > 1-4 columb interaction, because I am using FudgeQQ =1.0.And in > GROMOS96 and in ffgmx force field there is not separate set of > parameters for Columb14 interaction. am I correct?? Basically correct. However, there is never a second set of parameters for coulombic 1-4 interactions--it simply is not possible with gromacs-3.3.1, this is the central point that lead to the need for Tieleman's 2006 paper that is mentioned below. > Apart from that in one of your previous mail in gromacs mailing list > .subject : - OPLS and Berger lipid et al Tieleman 2006 > http://www.gromacs.org/pipermail/gmx-users/2006-August/023587.html > > you had mentioned > "However, this 2006 paper appears to be entirely different. If I > understand correctly, the main difference is that they "decided to > replace the 1-4 interactions in the lipids (both the electrostatic > and the Lennard-Jones components) with dihedral potentials.)" > because of the inability to scale columbic separately in Gromacs." > > So if we use FudgeQQ =0.5 there then what is the problem to direct > addition of berger lipid in OPLS force field?? because FudgeQQ is > going to apply on all the cases dosen't matter what we are using > genpair = yes or no.Why they have to replace the 1-4 interaction > with dihedral potential (RB). > The problem is that the FudgeQQ for the Berger lipids should be 1.0 and for OPLS-AA it should be 0.5. There is no way to do this analogously to the LJ parameters that can be set in [ pairs ] or [ pairtypes ]. If you want to base your work on something that has been entirely tested and published, then I suggest that you either live with the 0.5 FudgeQQ scaling for all, or request the new dihedrals from Tieleman's lab (although I believe that they are not yet being made available). If you can accept working with an idea that sounds rigorous but has not yet been tested for more than 5ns or published at all, look here for the method that I use: http://www.gromacs.org/pipermail/gmx-users/2006-September/023761.html and here for Berks much improved suggestion about clean implementaion: http://www.gromacs.org/pipermail/gmx-users/2006-September/023782.html (I am sure the set of zeroes in "with additional 0 0 parameters for the LJ" read sigma epsilon in some font.) > eagry waiting for your reply, > Alok > > ----- Original Message ----- > From: > To: > Sent: Thursday, September 21, 2006 2:05 AM > Subject: [gmx-users] 1-4 columb interaction > > > You are right that the LJ fudge values don't get applied if > gen-pairs=no. However, FudgeQQ is always applied. However, one would > hope that Qiao was correct and the main .itp files at least list the > correct scaling of LJ 1-4 interactions. Force fields that use > gen-pairs=no explicitly list 1-4 LJ parameters in the pairtypes > section. This appears to be the case in the gromos96 force field. For > example, > > [ nonbond_params ] > ; i j func c6 c12 > OM O 1 0.0022619536 7.4149321e-07 > [ pairtypes ] > ; i j func c6 c12 > OM O 1 0.0022619536 7.4149321e-07 > > So a 1-4 (pairtypes) and a 1->5 or nonbonded LJ are going to be the same. > > The treatment of 1-4 interactions is quite well described in the > gromacs manual. > > > ----- Original Message ----- > Thanks Qiao for your reply. > > But If I am using genpair = no (GROMOS 96 force field) then there is > no meaning of fudgeLJ and fudgeQQ (correct me if I am wrong). > > So more specific if I am using GROMOS96 force field then is there any > scaling for 1-4 columb interaction?? > if yes then how? > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php From oliver.stueker at uni-paderborn.de Thu Sep 21 16:57:29 2006 From: oliver.stueker at uni-paderborn.de (=?ISO-8859-1?Q?Oliver_St=FCker?=) Date: Thu, 21 Sep 2006 10:57:29 -0400 Subject: [gmx-users] Recover corrupted files from DVD In-Reply-To: <000a01c6dd61$cb175cf0$150110ac@gandalf> References: <000a01c6dd61$cb175cf0$150110ac@gandalf> Message-ID: <4512A859.3060607@uni-paderborn.de> Hi Nuno, > BTW, do you recommend any soft that I can use to try to try to > recover files froma CD/DVD (iso9600)? my favorite computer-magazine has once published a Windows-Software to extract a mostly complete ISO-image of a faulty CD/DVD. ftp://ftp.heise.de/pub/ct/ctsi/h2cdimage.zip The enclosed Documentation is only in German. a brief description: run in a command-Shell of Windows with: h2cdimage :: [-i] where "::" is the address of your DVD/CD-Drive: 0:0:0 - IDE Primary Master 0:1:0 - IDE Primary Slave 1:0:0 - IDE Secondary Master 1:1:0 - IDE Secondary Slave is the base-name of two created files .iso (DATA) and .h2i (STATUS) and -i tells the program to create new iso- and status-files h2cdimage will start to create an iso-image first with all healthy parts of the DVD before it will start spending time in reading faulty sectors. You can re-run the program several times while skipping the "-i" Option (you should try different Disc-Drives on different computers) It will store information of successfully recovered sectors in the .h2i file. Hopefully some drives can read sectors that other couldn't, depending on the automatic error correction in the DVD-Drives Firmware. If you know German (or have someone at hand who does) here's the online version of the article describing everything a bit more detailed: http://www.heise.de/ct/05/16/078/ Good luck... ...Oliver From ababakha at mccammon.ucsd.edu Thu Sep 21 19:07:03 2006 From: ababakha at mccammon.ucsd.edu (Arneh Babakhani) Date: Thu, 21 Sep 2006 10:07:03 -0700 Subject: [gmx-users] Minimization Issue - membrane inverted and system copied In-Reply-To: <001801c6dd9a$17ca16e0$65741aac@alok> References: <20060921093808.rxtkbuehnmf4ww44@webmail.utoronto.ca> <001801c6dd9a$17ca16e0$65741aac@alok> Message-ID: <4512C6B7.7000205@mccammon.ucsd.edu> Hi, I'm getting a quirky result from my minimization of my system (which consists of a small peptide in a membrane, solvated). When I look at the trr of the minimization (or the outputted structure after minization), I notice that my membrane has been inverted, and there are 4 copies of the system. (Yes, i have my images setting in VMD set for just the self structure). What's going on here? My structure, topology and mdp files are all correct (I successfully executed previous minimizations with them). I'm sure it's something really obvious, by I can't figure it out. Would appreciate any help. Regards, Arneh ; VARIOUS PREPROCESSING OPTIONS = title = cpp = /usr/bin/cpp include = define = -DFLEX_SPC ; RUN CONTROL PARAMETERS = integrator = steep ; start time and timestep in ps = tinit = 0 dt = 0.002 nsteps = 5000 ; mode for center of mass motion removal = comm-mode = Linear ; number of steps for center of mass motion removal = nstcomm = 1 ; group(s) for center of mass motion removal = comm-grps = ; LANGEVIN DYNAMICS OPTIONS = ; Temperature, friction coefficient (amu/ps) and random seed = bd-temp = 300 bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS = ; Force tolerance and initial step-size = emtol = 10 emstep = 0.01 ; Max number of iterations in relax_shells = niter = 20 ; Step size (1/ps^2) for minimization of flexible constraints = fcstep = 0 ; Frequency of steepest descents steps when doing CG = nstcgsteep = 1000 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 100 nstvout = 100 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 100 nstenergy = 100 ; Output frequency and precision for xtc file = nstxtcout = 0 xtc-precision = 1000 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = xtc-grps = ; Selection of energy groups = energygrps = ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or no = pbc = xyz ; nblist cut-off = rlist = 1 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.0 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r = 1 ; Method for doing Van der Waals = vdw-type = Cut-off ; cut-off lengths = rvdw-switch = 0 rvdw = 1.0 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters = pme_order = 4 ewald_rtol = 1e-5 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = yes ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = Tcoupl = no ; Groups to couple separately = tc-grps = ; Time constant (ps) and reference temperature (K) = tau-t = ref-t = ; Pressure coupling = Pcoupl = no Pcoupltype = Isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau-p = 1 compressibility = ref-p = ; SIMULATED ANNEALING CONTROL = annealing = no ; Time at which temperature should be zero (ps) = zero-temp_time = 0 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = no gen-temp = 300 gen-seed = 173529 ; OPTIONS FOR BONDS = constraints = none ; Type of constraint algorithm = constraint-algorithm = Lincs ; Do not constrain the start configuration = unconstrained-start = no ; Use successive overrelaxation to reduce the number of shake iterations = Shake-SOR = no ; Relative tolerance of shake = shake-tol = 1e-04 ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 4 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs-warnangle = 30 ; Convert harmonic bonds to morse potentials = morse = no ; ENERGY GROUP EXCLUSIONS = ; Pairs of energy groups for which all non-bonded interactions are excluded = energygrp_excl = ; NMR refinement stuff = ; Distance restraints type: No, Simple or Ensemble = disre = No ; Force weighting of pairs in one distance restraint: Conservative or Equal = disre-weighting = Conservative ; Use sqrt of the time averaged times the instantaneous violation = disre-mixed = no disre-fc = 1000 disre-tau = 0 ; Output frequency for pair distances to energy file = nstdisreout = 100 ; Orientation restraints: No or Yes = orire = no ; Orientation restraints force constant and tau for time averaging = orire-fc = 0 orire-tau = 0 orire-fitgrp = ; Output frequency for trace(SD) to energy file = nstorireout = 100 ; Free energy control stuff = free-energy = no init-lambda = 0 delta-lambda = 0 sc-alpha = 0 sc-sigma = 0.3 ; Non-equilibrium MD stuff = acc-grps = accelerate = freezegrps = freezedim = cos-acceleration = 0 ; Electric fields = ; Format is number of terms (int) and for all terms an amplitude (real) = ; and a phase angle (real) = E-x = E-xt = E-y = E-yt = E-z = E-zt = ; User defined thingies = user1-grps = user2-grps = userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 From p.biswas at csuohio.edu Thu Sep 21 19:54:30 2006 From: p.biswas at csuohio.edu (Pradip Kumar Biswas) Date: Thu, 21 Sep 2006 13:54:30 -0400 Subject: [gmx-users] running CPMD with GROMACS interface in SGI irix 6.5 In-Reply-To: <93e2edd90609121810x3631409fy8e44a8a78c346997@mail.gmail.com> References: <93e2edd90609121810x3631409fy8e44a8a78c346997@mail.gmail.com> Message-ID: <39c2335cb15f1f8bf5cdeeeb0a3edeb1@csuohio.edu> Hi James, It seems that the problem has no connection with QM/MM implementation and it is something related to CPMD compilation in your architecture. You can verify whether this is true by running the CPMD alone. If the problem persists, I suggest you to try without any optimization flag for the CPMD compiler and see if the problem gets over. If not, lets raise the issue in the CPMD mailing list with your configuration patch details. pb. On Sep 12, 2006, at 9:10 PM, james zhang wrote: > Hi > ? > I got some trouble in running CPMD with GROMACS?interface?in SGI irix > 6.5. Thanks in advance > ? > the error is > > ?[PEAK NUMBER? 116]?????? PEAK MEMORY????? 14169180 =? 113.4 MBytes > ?[ALL. NUMBER? 116]????? TOTAL MEMORY????? 13983696 =? 111.9 MBytes > ?================================================================== > > > ?PROGRAM STOPS IN SUBROUTINE MEMORY_CHECK|? CORRUPTED MEMORY [PROC=?? > 8] > ?EIGV???????? 390897072 CORRUPTED?? 390994624 CORRUPTED?????? 12193 > ?SC0????????? 390994640 CORRUPTED?? 391254032 CORRUPTED?????? 32423 > ?PME????????? 391254048 CORRUPTED?? 391513440 CORRUPTED?????? 32423 > ?GDE????????? 391513456 CORRUPTED?? 391772848 CORRUPTED?????? 32423 > ?HGPOT??????? 391860984 CORRUPTED?? 392180992 CORRUPTED?????? 40000 > ?HIPZ???????? 392181008 CORRUPTED?? 394741016 CORRUPTED????? 320000 > ?NZFFP??????? 394741032 CORRUPTED?? 396297320 CORRUPTED????? 194535 > ?NZFSP??????? 396297336 CORRUPTED?? 396987776 CORRUPTED?????? 86304 > ??? 396987792 CORRUPTED?? 403238296 CORRUPTED????? 781312 > ??? 403238312 CORRUPTED?? 416826464 CORRUPTED???? 1698518 > ?------------------------------------------------------------------ > ?[PEAK NUMBER? 116]?????? PEAK MEMORY????? 14169180 =? 113.4 MBytes > ?[ALL. NUMBER? 116]????? TOTAL MEMORY????? 13983696 =? 111.9 MBytes > ?================================================================== > > > ?PROGRAM STOPS IN SUBROUTINE MEMORY_CHECK|? CORRUPTED MEMORY [PROC=?? > 9] > ?[PEAK NUMBER? 116]?????? PEAK MEMORY????? 14169180 =? 113.4 MBytes > ?[ALL. NUMBER? 116]????? TOTAL MEMORY????? 13983696 =? 111.9 MBytes > ?================================================================== > > > ?PROGRAM STOPS IN SUBROUTINE MEMORY_CHECK|? CORRUPTED MEMORY [PROC=? > 10] > PC: 0xb18ca40 MPI_SGI_stacktraceback in /usr/lib64/libmpi.so > PC: 0xb1b5e30 PMPI_Abort in /usr/lib64/libmpi.so > PC: 0xb1e84b8 pmpi_abort_ in /usr/lib64/libmpi.so > PC: 0x10624edc stopgm in > /home/irix/meen/jzhang/qmmm/CPMD-3.11.1/SOURCE/cpmd.x > PC: 0x1049884c memory_check in > /home/irix/meen/jzhang/qmmm/CPMD-3.11.1/SOURCE/cpmd.x > PC: 0x1051866c testex in /home/irix/meen/jzhang/qmmm/CPMD- > 3.11.1/SOURCE/cpmd.x > PC: 0x10447cd4 updwf in > /home/irix/meen/jzhang/qmmm/CPMD-3.11.1/SOURCE/cpmd.x > PC: 0x10399770 interface in > /home/irix/meen/jzhang/qmmm/CPMD-3.11.1/SOURCE/cpmd.x > PC: 0x10633614 interpt in /home/irix/meen/jzhang/qmmm/CPMD- > 3.11.1/SOURCE/cpmd.x > PC: 0x10698438 cpmd in > /home/irix/meen/jzhang/qmmm/CPMD-3.11.1/SOURCE/cpmd.x > PC: 0x10698510 cpmd_stuttgart in > /home/irix/meen/jzhang/qmmm/CPMD-3.11.1/SOURCE/cpmd.x > PC: 0x291fc34 main in /usr/lib64/libftn.so > > > -- > Sincerely yours, > James jianzhang > Department of Mechanical and Chemical Engineering > North Carolina Agricultural and Technical State University > 1601 East Market Street > Greensboro, NC 27411 > ? > > > -- > Sincerely yours, > James jianzhang > Department of Mechanical and Chemical Engineering > North Carolina Agricultural and Technical State University > 1601 East Market Street > Greensboro, NC 27411 > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Pradip K. Biswas, PhD. Research Associate, Department of Chemistry; Cleveland State University, Ohio-44115 Phone: 1-216-875-9723 http://comppsi.csuohio.edu/groups/people/biswas.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 4050 bytes Desc: not available URL: From dmobley at gmail.com Thu Sep 21 20:07:28 2006 From: dmobley at gmail.com (David Mobley) Date: Thu, 21 Sep 2006 11:07:28 -0700 Subject: [gmx-users] Free energy for charged molecules In-Reply-To: <20060920072517.38044.qmail@web33008.mail.mud.yahoo.com> References: <20060920072517.38044.qmail@web33008.mail.mud.yahoo.com> Message-ID: Ignacio, > Is there some precaution or additional term I should take into account > when calculating the free energy of solvation for a charged molecule? > > I plan to make the molecule "disappear" whith lambda moving from 0 to 1 > and then perform a thermodynamical integration, this seems to work > reasonably well for neutral molecules. Is there any "gotcha" with > charged molecules? In my opinion, yes. This has been discussed some on the list before so I encourage you to search the archives. The basic problem is that, when using PME (as you are) the system must be net neutral. When you turn off or on a charge in your system, you are necessarily making the system charged. Most PME codes are actually designed to be able to handle this (in the sense of not exploding) by introducing a uniform neutralizing background charge to enforce neutrality. Unfortunately, this is actually problematic for free energy calculations: If you just turn off the charge on your molecule, instead of getting the free energy of turning off that charge, you're getting the free energy of turning off the charge plus the free energy of turning on a uniform neutralizing background charge, which is obviously not what you want. There have been some comments on the list suggesting that one might be able to subtract off this contribution by either (a) making a series of separate calls to PME (which would require code changes), or (b) doing a series of free energy calculations with the charges on various components of the system set to zero. I have a rough idea of how to do option (a), but h aven't been convinced yet that there is a rigorous way to do it, and option (b) sounds like it might be reasonable, but I again haven't been convinced it's rigorous, nor I have I seen any publications using this method. I would encourage you to dig in to this issue; in my opinion, it is a sufficiently large problem that I would not let someone publish a free energy calculation where they change the net charge of a system while using PME unless they can demonstrate that they have correctly handled this. (It will, of course, "work" to do it with the uniform neutralizing background charge. The only problem is that your answer will be wrong by some unknown amount which is likely to be fairly large.) Please let me know if you get anywhere on it: I'd love to be able to do these calculations on charged systems but so far don't have a way to do it (with PME) that I'm convinced is rigorous. Thanks, David Of course, I'm using PME, pbc=xyz and a large enough > simulation box. > > Thanks > > > > ___________________________________________________________ > To help you stay safe and secure online, we've developed the all new Yahoo! Security Centre. http://uk.security.yahoo.com > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > From tsjerkw at gmail.com Thu Sep 21 21:31:57 2006 From: tsjerkw at gmail.com (Tsjerk Wassenaar) Date: Thu, 21 Sep 2006 21:31:57 +0200 Subject: [gmx-users] Minimization Issue - membrane inverted and system copied In-Reply-To: <4512C6B7.7000205@mccammon.ucsd.edu> References: <20060921093808.rxtkbuehnmf4ww44@webmail.utoronto.ca> <001801c6dd9a$17ca16e0$65741aac@alok> <4512C6B7.7000205@mccammon.ucsd.edu> Message-ID: <8ff898150609211231n5ef1c4e4vf9e9f24b1c4d2491@mail.gmail.com> Hi Arneh, I guess it's the PBC. Did you center your bilayer at z=0 (or x, or y)? Then it's certain it's the PBC. Next time it may be better to center your system at the box center. Best, Tsjerk On 9/21/06, Arneh Babakhani wrote: > Hi, > > > I'm getting a quirky result from my minimization of my system (which > consists of a small peptide in a membrane, solvated). > > > When I look at the trr of the minimization (or the outputted structure > after minization), I notice that my membrane has been inverted, and > there are 4 copies of the system. (Yes, i have my images setting in VMD > set for just the self structure). > > > What's going on here? My structure, topology and mdp files are all > correct (I successfully executed previous minimizations with them). I'm > sure it's something really obvious, by I can't figure it out. Would > appreciate any help. > > > Regards, > > > Arneh > > > > ; VARIOUS PREPROCESSING OPTIONS = > title = > cpp = /usr/bin/cpp > include = > define = -DFLEX_SPC > > ; RUN CONTROL PARAMETERS = > integrator = steep > ; start time and timestep in ps = > tinit = 0 > dt = 0.002 > nsteps = 5000 > ; mode for center of mass motion removal = > comm-mode = Linear > ; number of steps for center of mass motion removal = > nstcomm = 1 > ; group(s) for center of mass motion removal = > comm-grps = > > ; LANGEVIN DYNAMICS OPTIONS = > ; Temperature, friction coefficient (amu/ps) and random seed = > bd-temp = 300 > bd-fric = 0 > ld-seed = 1993 > > ; ENERGY MINIMIZATION OPTIONS = > ; Force tolerance and initial step-size = > emtol = 10 > emstep = 0.01 > ; Max number of iterations in relax_shells = > niter = 20 > ; Step size (1/ps^2) for minimization of flexible constraints = > fcstep = 0 > ; Frequency of steepest descents steps when doing CG = > nstcgsteep = 1000 > > ; OUTPUT CONTROL OPTIONS = > ; Output frequency for coords (x), velocities (v) and forces (f) = > nstxout = 100 > nstvout = 100 > nstfout = 0 > ; Output frequency for energies to log file and energy file = > nstlog = 100 > nstenergy = 100 > ; Output frequency and precision for xtc file = > nstxtcout = 0 > xtc-precision = 1000 > ; This selects the subset of atoms for the xtc file. You can = > ; select multiple groups. By default all atoms will be written. = > xtc-grps = > ; Selection of energy groups = > energygrps = > > ; NEIGHBORSEARCHING PARAMETERS = > ; nblist update frequency = > nstlist = 10 > ; ns algorithm (simple or grid) = > ns_type = grid > ; Periodic boundary conditions: xyz or no = > pbc = xyz > ; nblist cut-off = > rlist = 1 > domain-decomposition = no > > ; OPTIONS FOR ELECTROSTATICS AND VDW = > ; Method for doing electrostatics = > coulombtype = PME > rcoulomb-switch = 0 > rcoulomb = 1.0 > ; Dielectric constant (DC) for cut-off or DC of reaction field = > epsilon_r = 1 > ; Method for doing Van der Waals = > vdw-type = Cut-off > ; cut-off lengths = > rvdw-switch = 0 > rvdw = 1.0 > ; Apply long range dispersion corrections for Energy and Pressure = > DispCorr = No > ; Spacing for the PME/PPPM FFT grid = > fourierspacing = 0.12 > ; FFT grid size, when a value is 0 fourierspacing will be used = > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > ; EWALD/PME/PPPM parameters = > pme_order = 4 > ewald_rtol = 1e-5 > ewald_geometry = 3d > epsilon_surface = 0 > optimize_fft = yes > > ; OPTIONS FOR WEAK COUPLING ALGORITHMS = > ; Temperature coupling = > Tcoupl = no > ; Groups to couple separately = > tc-grps = > ; Time constant (ps) and reference temperature (K) = > tau-t = > ref-t = > ; Pressure coupling = > Pcoupl = no > Pcoupltype = Isotropic > ; Time constant (ps), compressibility (1/bar) and reference P (bar) = > tau-p = 1 > compressibility = > ref-p = > > ; SIMULATED ANNEALING CONTROL = > annealing = no > ; Time at which temperature should be zero (ps) = > zero-temp_time = 0 > > ; GENERATE VELOCITIES FOR STARTUP RUN = > gen_vel = no > gen-temp = 300 > gen-seed = 173529 > > ; OPTIONS FOR BONDS = > constraints = none > ; Type of constraint algorithm = > constraint-algorithm = Lincs > ; Do not constrain the start configuration = > unconstrained-start = no > ; Use successive overrelaxation to reduce the number of shake iterations = > Shake-SOR = no > ; Relative tolerance of shake = > shake-tol = 1e-04 > ; Highest order in the expansion of the constraint coupling matrix = > lincs-order = 4 > ; Lincs will write a warning to the stderr if in one step a bond = > ; rotates over more degrees than = > lincs-warnangle = 30 > ; Convert harmonic bonds to morse potentials = > morse = no > > ; ENERGY GROUP EXCLUSIONS = > ; Pairs of energy groups for which all non-bonded interactions are > excluded = > energygrp_excl = > > ; NMR refinement stuff = > ; Distance restraints type: No, Simple or Ensemble = > disre = No > ; Force weighting of pairs in one distance restraint: Conservative or > Equal = > disre-weighting = Conservative > ; Use sqrt of the time averaged times the instantaneous violation = > disre-mixed = no > disre-fc = 1000 > disre-tau = 0 > ; Output frequency for pair distances to energy file = > nstdisreout = 100 > ; Orientation restraints: No or Yes = > orire = no > ; Orientation restraints force constant and tau for time averaging = > orire-fc = 0 > orire-tau = 0 > orire-fitgrp = > ; Output frequency for trace(SD) to energy file = > nstorireout = 100 > > ; Free energy control stuff = > free-energy = no > init-lambda = 0 > delta-lambda = 0 > sc-alpha = 0 > sc-sigma = 0.3 > > ; Non-equilibrium MD stuff = > acc-grps = > accelerate = > freezegrps = > freezedim = > cos-acceleration = 0 > > ; Electric fields = > ; Format is number of terms (int) and for all terms an amplitude (real) = > ; and a phase angle (real) = > E-x = > E-xt = > E-y = > E-yt = > E-z = > E-zt = > > ; User defined thingies = > user1-grps = > user2-grps = > userint1 = 0 > userint2 = 0 > userint3 = 0 > userint4 = 0 > userreal1 = 0 > userreal2 = 0 > userreal3 = 0 > userreal4 = 0 > > > > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 From zhoumadison at gmail.com Thu Sep 21 21:52:24 2006 From: zhoumadison at gmail.com (Lei Zhou) Date: Thu, 21 Sep 2006 15:52:24 -0400 Subject: [gmx-users] Extracting C-alpha component from all-atom Hessian matrix Message-ID: Dear GMX-users, I have been working on extracting the C-alpha component from the all-atom Hessian matrix, according to the equation proposed initially by Berk, H'=Hxx-HxyHyy-1Hyx. It worked quite nice in my hand and for a test protein, there is almost no visual difference in the confromational changes described by the eigenvectors between two methods (all-atom normal mode or C-alpha only). I am wondering whether there is a reference for this equation? Is it based on Gram-Schmidt formula for deriving a new set of vectors? There was a old paper by Brooks and Karplus (J. Comp. Chem., 1995) gave a detailed description of the normal mode analysis and prosposed a methods for extracting dihedral angle normal modes. So is there any difference between the method they proposed and equation mentioned above? Thank you for the help. Lei Zhou Columbia University [gmx-users] Normal Mode Analysis on Calphas only ?? *Berk Hess* gmx3 at hotmail.com *Wed May 18 08:42:23 CEST 2005* - Previous message: [gmx-users] Normal Mode Analysis on Calphas only ?? - Next message: [gmx-users] Normal Mode Analysis on Calphas only ?? - *Messages sorted by:* [ date ] [ thread ] [ subject ] [ author ] ------------------------------ Here is the formula (thanks to Herman Berendsen). I was slightly wrong. You first need to reduce the Hessian and then diagonalize the C-alpha only Hessian. definitions: Interesting particle coordinates: x Uninsteresting particle coordinates y full hessian in terms of (x, y): H Split H into four blocks: Hxx Hxy H = Hyx Hyy Then the hessian H' in the subspace of x coordinates, under the condition that the y coordinates are in a minimum, is H' = Hxx - Hxy Hyy^-1 Hyx This is a simple transformation, requiring only one inversion and two matrix multiplications. Berk. _________________________________________________________________ FREE pop-up blocking with the new MSN Toolbar - get it now! http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From ababakha at mccammon.ucsd.edu Thu Sep 21 21:58:04 2006 From: ababakha at mccammon.ucsd.edu (Arneh Babakhani) Date: Thu, 21 Sep 2006 12:58:04 -0700 Subject: [gmx-users] Minimization Issue - membrane inverted and system copied In-Reply-To: <8ff898150609211231n5ef1c4e4vf9e9f24b1c4d2491@mail.gmail.com> References: <20060921093808.rxtkbuehnmf4ww44@webmail.utoronto.ca> <001801c6dd9a$17ca16e0$65741aac@alok> <4512C6B7.7000205@mccammon.ucsd.edu> <8ff898150609211231n5ef1c4e4vf9e9f24b1c4d2491@mail.gmail.com> Message-ID: <4512EECC.6060901@mccammon.ucsd.edu> Ahh! Yes, Indeed I did center it to 0 0 0. I corrected that (centered it in the box), and it works fine now. Thanks Tsjerk, Regards, Arneh Tsjerk Wassenaar wrote: > Hi Arneh, > > I guess it's the PBC. Did you center your bilayer at z=0 (or x, or y)? > Then it's certain it's the PBC. Next time it may be better to center > your system at the box center. > > Best, > > Tsjerk > > On 9/21/06, Arneh Babakhani wrote: >> Hi, >> >> >> I'm getting a quirky result from my minimization of my system (which >> consists of a small peptide in a membrane, solvated). >> >> >> When I look at the trr of the minimization (or the outputted structure >> after minization), I notice that my membrane has been inverted, and >> there are 4 copies of the system. (Yes, i have my images setting in VMD >> set for just the self structure). >> >> >> What's going on here? My structure, topology and mdp files are all >> correct (I successfully executed previous minimizations with them). I'm >> sure it's something really obvious, by I can't figure it out. Would >> appreciate any help. >> >> >> Regards, >> >> >> Arneh >> >> >> >> ; VARIOUS PREPROCESSING OPTIONS = >> title = >> cpp = /usr/bin/cpp >> include = >> define = -DFLEX_SPC >> >> ; RUN CONTROL PARAMETERS = >> integrator = steep >> ; start time and timestep in ps = >> tinit = 0 >> dt = 0.002 >> nsteps = 5000 >> ; mode for center of mass motion removal = >> comm-mode = Linear >> ; number of steps for center of mass motion removal = >> nstcomm = 1 >> ; group(s) for center of mass motion removal = >> comm-grps = >> >> ; LANGEVIN DYNAMICS OPTIONS = >> ; Temperature, friction coefficient (amu/ps) and random seed = >> bd-temp = 300 >> bd-fric = 0 >> ld-seed = 1993 >> >> ; ENERGY MINIMIZATION OPTIONS = >> ; Force tolerance and initial step-size = >> emtol = 10 >> emstep = 0.01 >> ; Max number of iterations in relax_shells = >> niter = 20 >> ; Step size (1/ps^2) for minimization of flexible constraints = >> fcstep = 0 >> ; Frequency of steepest descents steps when doing CG = >> nstcgsteep = 1000 >> >> ; OUTPUT CONTROL OPTIONS = >> ; Output frequency for coords (x), velocities (v) and forces (f) = >> nstxout = 100 >> nstvout = 100 >> nstfout = 0 >> ; Output frequency for energies to log file and energy file = >> nstlog = 100 >> nstenergy = 100 >> ; Output frequency and precision for xtc file = >> nstxtcout = 0 >> xtc-precision = 1000 >> ; This selects the subset of atoms for the xtc file. You can = >> ; select multiple groups. By default all atoms will be written. = >> xtc-grps = >> ; Selection of energy groups = >> energygrps = >> >> ; NEIGHBORSEARCHING PARAMETERS = >> ; nblist update frequency = >> nstlist = 10 >> ; ns algorithm (simple or grid) = >> ns_type = grid >> ; Periodic boundary conditions: xyz or no = >> pbc = xyz >> ; nblist cut-off = >> rlist = 1 >> domain-decomposition = no >> >> ; OPTIONS FOR ELECTROSTATICS AND VDW = >> ; Method for doing electrostatics = >> coulombtype = PME >> rcoulomb-switch = 0 >> rcoulomb = 1.0 >> ; Dielectric constant (DC) for cut-off or DC of reaction field = >> epsilon_r = 1 >> ; Method for doing Van der Waals = >> vdw-type = Cut-off >> ; cut-off lengths = >> rvdw-switch = 0 >> rvdw = 1.0 >> ; Apply long range dispersion corrections for Energy and Pressure = >> DispCorr = No >> ; Spacing for the PME/PPPM FFT grid = >> fourierspacing = 0.12 >> ; FFT grid size, when a value is 0 fourierspacing will be used = >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> ; EWALD/PME/PPPM parameters = >> pme_order = 4 >> ewald_rtol = 1e-5 >> ewald_geometry = 3d >> epsilon_surface = 0 >> optimize_fft = yes >> >> ; OPTIONS FOR WEAK COUPLING ALGORITHMS = >> ; Temperature coupling = >> Tcoupl = no >> ; Groups to couple separately = >> tc-grps = >> ; Time constant (ps) and reference temperature (K) = >> tau-t = >> ref-t = >> ; Pressure coupling = >> Pcoupl = no >> Pcoupltype = Isotropic >> ; Time constant (ps), compressibility (1/bar) and reference P (bar) = >> tau-p = 1 >> compressibility = >> ref-p = >> >> ; SIMULATED ANNEALING CONTROL = >> annealing = no >> ; Time at which temperature should be zero (ps) = >> zero-temp_time = 0 >> >> ; GENERATE VELOCITIES FOR STARTUP RUN = >> gen_vel = no >> gen-temp = 300 >> gen-seed = 173529 >> >> ; OPTIONS FOR BONDS = >> constraints = none >> ; Type of constraint algorithm = >> constraint-algorithm = Lincs >> ; Do not constrain the start configuration = >> unconstrained-start = no >> ; Use successive overrelaxation to reduce the number of shake >> iterations = >> Shake-SOR = no >> ; Relative tolerance of shake = >> shake-tol = 1e-04 >> ; Highest order in the expansion of the constraint coupling matrix = >> lincs-order = 4 >> ; Lincs will write a warning to the stderr if in one step a bond = >> ; rotates over more degrees than = >> lincs-warnangle = 30 >> ; Convert harmonic bonds to morse potentials = >> morse = no >> >> ; ENERGY GROUP EXCLUSIONS = >> ; Pairs of energy groups for which all non-bonded interactions are >> excluded = >> energygrp_excl = >> >> ; NMR refinement stuff = >> ; Distance restraints type: No, Simple or Ensemble = >> disre = No >> ; Force weighting of pairs in one distance restraint: Conservative or >> Equal = >> disre-weighting = Conservative >> ; Use sqrt of the time averaged times the instantaneous violation = >> disre-mixed = no >> disre-fc = 1000 >> disre-tau = 0 >> ; Output frequency for pair distances to energy file = >> nstdisreout = 100 >> ; Orientation restraints: No or Yes = >> orire = no >> ; Orientation restraints force constant and tau for time averaging = >> orire-fc = 0 >> orire-tau = 0 >> orire-fitgrp = >> ; Output frequency for trace(SD) to energy file = >> nstorireout = 100 >> >> ; Free energy control stuff = >> free-energy = no >> init-lambda = 0 >> delta-lambda = 0 >> sc-alpha = 0 >> sc-sigma = 0.3 >> >> ; Non-equilibrium MD stuff = >> acc-grps = >> accelerate = >> freezegrps = >> freezedim = >> cos-acceleration = 0 >> >> ; Electric fields = >> ; Format is number of terms (int) and for all terms an amplitude >> (real) = >> ; and a phase angle (real) = >> E-x = >> E-xt = >> E-y = >> E-yt = >> E-z = >> E-zt = >> >> ; User defined thingies = >> user1-grps = >> user2-grps = >> userint1 = 0 >> userint2 = 0 >> userint3 = 0 >> userint4 = 0 >> userreal1 = 0 >> userreal2 = 0 >> userreal3 = 0 >> userreal4 = 0 >> >> >> >> >> _______________________________________________ >> gmx-users mailing list gmx-users at gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-request at gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > From MichaelOwen at creighton.edu Thu Sep 21 23:27:57 2006 From: MichaelOwen at creighton.edu (Owen, Michael) Date: Thu, 21 Sep 2006 16:27:57 -0500 Subject: [gmx-users] VAL group Message-ID: <80C4D42673F70F4B9333B9F3AFFCC5081D881E@EXBE06.blue.jays.creighton.edu> Hello fellow gmx users, when I convert a pdb file of a peptide that contains a valyl residue into a .gro file a separate "group" is made for the atoms in the valyl residue. This has happened when OPLSAA/l and the GROMOS96 53a6 force fields were used. The molecule appears as one in the topology file, and the atomic description of the valyl residue in the pdb file matches that of the ffoplsa.rtp file. An excert from the topology file that shows the structure contains one peptide is below. [ system ] ; Name Protein in water [ molecules ] ; Compound #mols Protein 1 SOL 6973 An excerpt from the index file that shows the VAL group containing 16 atoms is below. 28125 28126 28127 28128 28129 28130 28131 28132 28133 28134 28135 28136 28137 28138 28139 28140 28141 28142 28143 28144 28145 28146 28147 28148 28149 28150 28151 28152 28153 28154 28155 28156 28157 28158 28159 28160 28161 28162 [ VAL ] 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 [ SOL ] 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 Could something be wrong with the pdb2gmx program? Thank you in advance for any suggestions. Sincerely, Michael Owen -------------- next part -------------- An HTML attachment was scrubbed... URL: From yanmaocai at 126.com Fri Sep 22 05:32:51 2006 From: yanmaocai at 126.com (M. Yan) Date: Fri, 22 Sep 2006 11:32:51 +0800 (CST) Subject: [gmx-users] calculate the interaction energy between different parts of protein Message-ID: <45135963.0000FE.01695@bj126app19.126.com> Hi dear friends, I want to analyze the interaction energy between two parts of protein, for instance, residue 57-62 and residue 104-109. g_energy does not work because the file ener.edr did not record this items. How to calculate it from the trajectory file? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Mark.Abraham at anu.edu.au Fri Sep 22 05:41:07 2006 From: Mark.Abraham at anu.edu.au (Mark Abraham) Date: Fri, 22 Sep 2006 13:41:07 +1000 Subject: [gmx-users] calculate the interaction energy between different parts of protein In-Reply-To: <45135963.0000FE.01695@bj126app19.126.com> References: <45135963.0000FE.01695@bj126app19.126.com> Message-ID: <45135B53.6050605@anu.edu.au> M. Yan wrote: > Hi dear friends, > I want to analyze the interaction energy between two parts of protein, > for instance, residue 57-62 and residue 104-109. g_energy does not work > because the file ener.edr did not record this items. How to calculate > it from the trajectory file? Define appropriate energy groups, then use mdrun -rerun. Mark From toma0052 at umn.edu Fri Sep 22 06:29:24 2006 From: toma0052 at umn.edu (toma0052) Date: Thu, 21 Sep 2006 23:29:24 CDT Subject: [gmx-users] Lipid simulations Message-ID: <200609220429.k8M4TOHi004410@vendetta.software.umn.edu> Hello, I am just starting MD simulations of lipid bilayers using Gromacs. I am looking to add a force to a cetain set of atoms, one layer of a bilayer. I was wondering in anyone knew what program files I would need to modify in order to do this. Thanks, Mike Tomasini From Mark.Abraham at anu.edu.au Fri Sep 22 06:55:19 2006 From: Mark.Abraham at anu.edu.au (Mark Abraham) Date: Fri, 22 Sep 2006 14:55:19 +1000 Subject: [gmx-users] Lipid simulations In-Reply-To: <200609220429.k8M4TOHi004410@vendetta.software.umn.edu> References: <200609220429.k8M4TOHi004410@vendetta.software.umn.edu> Message-ID: <45136CB7.8010803@anu.edu.au> toma0052 wrote: > Hello, > I am just starting MD simulations of lipid bilayers using Gromacs. I > am looking to add a force to a cetain set of atoms, one layer of a bilayer. > I was wondering in anyone knew what program files I would need to modify > in order to do this. No source code, most likely. You want to read chapters 4 and 5 of the manual. Mark From Mark.Abraham at anu.edu.au Fri Sep 22 07:52:19 2006 From: Mark.Abraham at anu.edu.au (Mark Abraham) Date: Fri, 22 Sep 2006 15:52:19 +1000 Subject: [gmx-users] question about energy and pressure In-Reply-To: <6a91f07b0609200513g5c404d49gd5e5e8f784afd0b6@mail.gmail.com> References: <6a91f07b0609200513g5c404d49gd5e5e8f784afd0b6@mail.gmail.com> Message-ID: <45137A13.3090809@anu.edu.au> Qiao Baofu wrote: > Hi all, > > I have some questions about the gromacs: > > 1. I simualted a pure small molecule system. All the simulation is ok. > But when I use g_energy to calculate the energy of bond, angle, lj, and > coloumb, it gives the following energy. The energies is much bigger, > about 50-100 times bigger than the reported data. What's wrong? What is this "reported data"? > Statistics over 5000001 steps [ 0.0000 thru 5000.0000 ps ], 6 data sets > > Energy Average RMSD Fluct. Drift > Tot-Drift > ------------------------------------------------------------------------------- > > Bond 2869.13 93.6564 93.6562 0.000137548 > 0.687742 > Angle 7303.46 140.13 140.13 0.000189867 > 0.949334 > Ryckaert-Bell. 3326.2 97.6245 97.6161 -0.000890977 -4.45489 > LJ-(SR) -7616.62 138.684 138.67 -0.00138166 > -6.90831 > Coulomb-(SR) -22763.2 138.465 138.238 -0.00549019 -27.451 > Potential -64743 219.54 219.203 -0.00842365 > -42.1182 > > 2. I used the "isotropic!!" pressure coupling, but at the end of the > .log file (in the average section), it says: > > Pressure (bar) > -2.64364e+01 3.71622e+01 3.00738e+00 > 3.71622e+01 1.32932e+01 -2.49814e+01 > 3.00738e+00 -2.49814e+01 1.61609e+01 > > The Pxx, Pyy, Pzz are not equal. Why? What is the geometry of your system? Mark From arindamganguly at gmail.com Fri Sep 22 08:48:21 2006 From: arindamganguly at gmail.com (Arindam Ganguly) Date: Fri, 22 Sep 2006 01:48:21 -0500 Subject: [gmx-users] g_confrms_d Message-ID: Hi Gmx-users in the manual of GROMACS 3.3 for the g_confrms , the manual states the following. " g confrms computes the root mean square deviation (RMSD) of two structures after LSQ fitting the second structure on the first one. " anybody has references to LSQ method ? thanks very much. Arindam Ganguly -------------- next part -------------- An HTML attachment was scrubbed... URL: From Mark.Abraham at anu.edu.au Fri Sep 22 09:11:32 2006 From: Mark.Abraham at anu.edu.au (Mark Abraham) Date: Fri, 22 Sep 2006 17:11:32 +1000 Subject: [gmx-users] g_confrms_d In-Reply-To: References: Message-ID: <45138CA4.50104@anu.edu.au> Arindam Ganguly wrote: > Hi Gmx-users > in the manual of GROMACS 3.3 for the g_confrms , the manual states the > following. > > " g confrms computes the root mean square deviation (RMSD) of two > structures after LSQ fitting the second > > structure on the first one. " > > anybody has references to LSQ method ? thanks very much. Authors who've written independently on these topics include W Kabsch, R Diamond, S K Kearsley, going back to 1976. Bring your memories of undergraduate mathematics. :-) Mark From jellby at yahoo.com Fri Sep 22 09:37:47 2006 From: jellby at yahoo.com (=?iso-8859-1?q?Ignacio=20Fern=E1ndez=20Galv=E1n?=) Date: Fri, 22 Sep 2006 08:37:47 +0100 (BST) Subject: [gmx-users] Free energy for charged molecules In-Reply-To: Message-ID: <20060922073747.46947.qmail@web33001.mail.mud.yahoo.com> --- David Mobley wrote: > > Is there any "gotcha" with charged molecules? > > In my opinion, yes. This has been discussed some on the list before > so > I encourage you to search the archives. The basic problem is that, > when using PME (as you are) the system must be net neutral. When you > turn off or on a charge in your system, you are necessarily making > the > system charged. Most PME codes are actually designed to be able to > handle this (in the sense of not exploding) by introducing a uniform > neutralizing background charge to enforce neutrality. Thanks for your reply. I had actually search the archives but didn't find any clear answer (maybe the search was not so good)... You mention this is a problem with PME, would plain Ewald or even Reaction-Field be less problematic in this case? And how large do you estimate the cutoff should be to give reasonable results? My system is a small molecule (~20 atoms) in water, so I can afford building boxes with a lot of solvent. Thanks, Ignacio Fern?ndez Galv?n ___________________________________________________________ All new Yahoo! Mail "The new Interface is stunning in its simplicity and ease of use." - PC Magazine http://uk.docs.yahoo.com/nowyoucan.html From akshay17 at olemiss.edu Wed Sep 20 23:48:42 2006 From: akshay17 at olemiss.edu (Akshay Patny) Date: Wed, 20 Sep 2006 16:48:42 -0500 Subject: [gmx-users] Which POPC Bilayer to start? Message-ID: <000d01c6dcfe$8eab1b20$8aa74a82@Plasma> Hi All I am trying to use POPC bilayer for doing GPCR simulation. I have come across two options of generating a POPC bilayer >>>> 1. I can generate a POPC bilayer from the VMD Membrane plug-in, wherein the membrane is generated from the pre-built membrane square patches and lipid tails are (almost) fully extended. 2. Alternatively, I can download the pre-equilibrated POPC bilayer from Dr. Tieleman's website, http://moose.bio.ucalgary.ca/index.php?page=People Since, I am new to the GPCR-membrane modeling, can you suggest me which out of the above two options can be a better starting point for the simulation of my GPCR protein? A membrane generated from VMD or a pre-equilibrated membrane?? Would the equilibration time for my protein be lesser in one out of the two? If option 2 is a good idea then out of popc128a.pdb and popc128b.pdb (both available from Prof. Tieleman's website), which will be a better model to start with? Thank you very much in advance. Akshay Akshay Patny Graduate Research Assistant Faser Hall 417, Department of Medicinal Chemistry Research Institute of Pharmaceutical Sciences University of Mississippi University, MS 38677 E-mail: akshay17 at olemiss.edu Tel: 662-915-1286 (office); Web: www.olemiss.edu From yanmaocai at 126.com Fri Sep 22 09:58:23 2006 From: yanmaocai at 126.com (M. Yan) Date: Fri, 22 Sep 2006 15:58:23 +0800 (CST) Subject: [gmx-users] calculate the interaction energy between differentparts of protein Message-ID: <4513979F.00002A.18484@bj126app17.126.com> Thank you, Mark I modify the .mdp file as follows: energygrps = Protein sol Cl --> energygrps = res57_62 res102_109 and make tpr file: grompp -f md.mdp -c pr_out.gro -p topol.top -o rerun.tpr -n index.ndx mdrun -rerun test.xtc -s rerun.tpr It gives warings: WARNING: Some frames do not contain velocities. Ekin, temperature and pressure are incorrect, the virial will be incorrect when constraints are present. I found files traj.trr and ener.edr; However, I am not certain whether I did right? Is any extra constraints needed? From: "Mark Abraham" Sent :2006-09-22 11:41:07 To:"Discussion list for GROMACS users" Title: Re: [gmx-users] calculate the interaction energy between different parts of protein M. Yan wrote: > Hi dear friends, > I want to analyze the interaction energy between two parts of protein, > for instance, residue 57-62 and residue 104-109. g_energy does not work > because the file ener.edr did not record this items. How to calculate > it from the trajectory file? Define appropriate energy groups, then use mdrun -rerun. Mark _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -------------- next part -------------- An HTML attachment was scrubbed... URL: From yanmaocai at 126.com Fri Sep 22 08:59:22 2006 From: yanmaocai at 126.com (M. Yan) Date: Fri, 22 Sep 2006 14:59:22 +0800 (CST) Subject: [gmx-users] calculate the interac tion energy between different parts of pr otein In-Reply-To: <45135B53.6050605@anu.edu.au> References: <45135963.0000FE.01695@bj126app19.126.com> <45135B53.6050605@anu.edu.au> Message-ID: <451389CA.00003D.23354@bj126app19.126.com> Thank you, Mark I modify the .mdp file as follows: energygrps = Protein sol Cl --> energygrps = res57_62 res102_109 and make tpr file: grompp -f md.mdp -c pr_out.gro -p topol.top -o rerun.tpr -n index.ndx mdrun -rerun test.xtc -s rerun.tpr It gives warings: WARNING: Some frames do not contain velocities. Ekin, temperature and pressure are incorrect, the virial will be incorrect when constraints are present. I found files traj.trr and ener.edr; However, I am not certain whether I did right? Is any extra constraints needed? From: "Mark Abraham" Sent :2006-09-22 11:41:07 To:"Discussion list for GROMACS users" Title: Re: [gmx-users] calculate the interaction energy between different parts of protein M. Yan wrote: > Hi dear friends, > I want to analyze the interaction energy between two parts of protein, > for instance, residue 57-62 and residue 104-109. g_energy does not work > because the file ener.edr did not record this items. How to calculate > it from the trajectory file? Define appropriate energy groups, then use mdrun -rerun. Mark _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -------------- next part -------------- An HTML attachment was scrubbed... URL: From dmobley at gmail.com Fri Sep 22 14:55:30 2006 From: dmobley at gmail.com (David Mobley) Date: Fri, 22 Sep 2006 05:55:30 -0700 Subject: [gmx-users] Free energy for charged molecules In-Reply-To: <20060922073747.46947.qmail@web33001.mail.mud.yahoo.com> References: <20060922073747.46947.qmail@web33001.mail.mud.yahoo.com> Message-ID: Ignacio, > Thanks for your reply. I had actually search the archives but didn't > find any clear answer (maybe the search was not so good)... You mention > this is a problem with PME, would plain Ewald or even Reaction-Field be > less problematic in this case? And how large do you estimate the cutoff > should be to give reasonable results? My system is a small molecule > (~20 atoms) in water, so I can afford building boxes with a lot of > solvent. Sorry, instead of PME, I should have said "lattice sum electrostatics", which all have the same requirement that the system be net neutral. Things are different with reaction field, but it is still not clear that one gets the "right answer". There is a recent paper which has been mentioned on the list by Hunenberger, I believe, which computes the hydration free energy of a sodium ion with several different methods including lattice-sum and reaction field and gets the same answer by applying appropriate corrections. But so far I haven't been able to understand it. You might want to look that one up. Again, don't just assume that if you use the right treatment of electrostatics it will just "work" in the sense of giving you the right answer: Things seem to be far more complicated than that. David > Thanks, > Ignacio Fern?ndez Galv?n > > > > > > ___________________________________________________________ > All new Yahoo! Mail "The new Interface is stunning in its simplicity and ease of use." - PC Magazine > http://uk.docs.yahoo.com/nowyoucan.html > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > From quantrum75 at yahoo.com Fri Sep 22 17:10:17 2006 From: quantrum75 at yahoo.com (Rama Gullapalli) Date: Fri, 22 Sep 2006 08:10:17 -0700 (PDT) Subject: [gmx-users] g_rotacf In-Reply-To: Message-ID: <20060922151017.72769.qmail@web31412.mail.mud.yahoo.com> Hello everybody, I have nearly 100 different vectors to analyse using g_rotacf. I was wondering if there was anyway to do this in GROMACS simultaneously since g_rotacf does not have have the -ng option like in g_traj or others. I would imagine one could use a awk script to run g_rotacf to run a hundred times, but I am not sure how to go about it. If anyone can provide me with pointers on that it would be great Thanks in advance Rama --------------------------------- Talk is cheap. Use Yahoo! Messenger to make PC-to-Phone calls. Great rates starting at 1?/min. -------------- next part -------------- An HTML attachment was scrubbed... URL: From spoel at xray.bmc.uu.se Fri Sep 22 18:22:29 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Fri, 22 Sep 2006 18:22:29 +0200 (CEST) Subject: [gmx-users] g_rotacf In-Reply-To: <20060922151017.72769.qmail@web31412.mail.mud.yahoo.com> Message-ID: On Fri, 22 Sep 2006, Rama Gullapalli wrote: >Hello everybody, > > I have nearly 100 different vectors to analyse using g_rotacf. I was wondering if there was anyway to do this in GROMACS simultaneously since g_rotacf does not have have the -ng option like in g_traj or others. > -noaver > I would imagine one could use a awk script to run g_rotacf to run a hundred times, but I am not sure how to go about it. If anyone can provide me with pointers on that it would be great > > Thanks in advance > Rama > > >--------------------------------- >Talk is cheap. Use Yahoo! Messenger to make PC-to-Phone calls. Great rates starting at 1?/min. -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From fujisaki at bu.edu Fri Sep 22 23:19:29 2006 From: fujisaki at bu.edu (Hiroshi Fujisaki) Date: Fri, 22 Sep 2006 17:19:29 -0400 Subject: [gmx-users] execution of water tutorial files on BG/L In-Reply-To: <20060920200039.7D95.FUJISAKI@bu.edu> References: <20060920200039.7D95.FUJISAKI@bu.edu> Message-ID: <20060922171242.7DA3.FUJISAKI@bu.edu> Dear gromacs users, I doubt that the following error message means that a right executable for BG/L is not created. Note that I here tried to install gromacs in our BlueGene facility. I also tried to compile the parallel version with --enable-mpi suffix, but I failed with an error message "checking size of int... configure: error: cannot compute sizeof (int), 77" So could someone give me the right configure file for BlueGene? Or is there any option for BlueGene? I appreciate your help. Best wishes, > Dear Gromacs users, > > After installing fftw-3.1.2 and gromacs itself on our > BlueGene facility, I am testing the tutorial > files, but I fail when I try all of them. For example, > for the water case (.../share/gromacs/tutor/water), > "grompp -v" seems to work, but "mdrun -v" suddenly > stops with the following message > "Illegal instruction" > > I've never experienced this when I use gromacs in > a linux machine. Could you suggest something? > The gromacs was compiled with a single precision > and single CPU version. > > I appreciate your help. > > Best wishes, > > -- > Hiroshi Fujisaki > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Hiroshi Fujisaki From zzhwise1 at 163.com Sat Sep 23 06:33:01 2006 From: zzhwise1 at 163.com (zzhwise1) Date: Sat, 23 Sep 2006 12:33:01 +0800 (CST) Subject: [gmx-users] about box size Message-ID: <4514B8FD.00001F.12562@bj163app78.163.com> hi everyone my system contain 2 monolayers,and it is more then 6nm in the z direction,and my box is 3.000,3.000,3.000, so it always wrong when mdrun,it said the box only this size,i want to know how to resolve my quetion ? thanks! -------------- next part -------------- An HTML attachment was scrubbed... URL: From chris.neale at utoronto.ca Sat Sep 23 07:38:32 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Sat, 23 Sep 2006 01:38:32 -0400 Subject: [gmx-users] about box size Message-ID: <20060923013832.zftylv9rbfwos8so@webmail.utoronto.ca> editconf -f in.gro -o out.gro -d 0.0 -bt cubic ---original message--- hi everyone my system contain 2 monolayers,and it is more then 6nm in the z direction,and my box is 3.000,3.000,3.000, so it always wrong when mdrun,it said the box only this size,i want to know how to resolve my quetion ? thanks! From zzhwise1 at 163.com Sat Sep 23 08:23:27 2006 From: zzhwise1 at 163.com (zzhwise1) Date: Sat, 23 Sep 2006 14:23:27 +0800 (CST) Subject: [gmx-users] about box size (II) Message-ID: <4514D2DF.0000E7.16859@bj163app78.163.com> thanks chris.neale! when i change the size to 6.0 (my system is 3,2,6) ,the upper monolayer turn around ,the bottom to the top ,top to the bottom ,is it the too big size in the x and y direction? should i to enlarge my sysytem to (6,6,6) to suit the box size? thanks! -------------- next part -------------- An HTML attachment was scrubbed... URL: From chris.neale at utoronto.ca Sat Sep 23 11:17:27 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Sat, 23 Sep 2006 05:17:27 -0400 Subject: [gmx-users] about box size (II) Message-ID: <20060923051727.vk1icpxzl1c00800@webmail.utoronto.ca> > when i change the size to 6.0 (my system is 3,2,6) > ,the upper monolayer turn around ,the bottom to the top ,top to the > bottom ,is it the too big size in the x and y direction? should i to > enlarge my sysytem to (6,6,6) to suit the box size? > thanks! Did you try the -d option that I suggested? It sounds like you used the -box option. Simply use the -d option. Choosing the membrane group for centering may leave you with a representation that is more intuitive. You should not need to do this next part, but if you want to you can check the min and max values for x,y, and z in your .gro file like this: 1. copy the following script into a file called maxmin.pl 2. chmod +x maxmin.pl 3. ./maxmin.pl structure.gro #!/bin/bash minx=`sort -n -k 4 $1 | head -1 | awk '{print $4}'` miny=`sort -n -k 5 $1 | head -1 | awk '{print $5}'` minz=`sort -n -k 6 $1 | head -1 | awk '{print $6}'` maxx=`sort -n -k 4 $1 | tail -1 | awk '{print $4}'` maxy=`sort -n -k 5 $1 | tail -1 | awk '{print $5}'` maxz=`sort -n -k 6 $1 | tail -1 | awk '{print $6}'` echo "x[$minx to $maxx] y[$miny to $maxy] z[$minz to $maxz]" From J.F.Hanna at warwick.ac.uk Sat Sep 23 16:59:35 2006 From: J.F.Hanna at warwick.ac.uk (Joanne Hanna) Date: Sat, 23 Sep 2006 15:59:35 +0100 Subject: [gmx-users] Changing output frequency when doing a continuation with tpbconv Message-ID: Hi I was wondering if you can change the output frequency of coordinates written to the *.trr file when you are doing continuation runs using tpbconv. Thanks Jo Joanne Hanna Department of Chemistry University of Warwick Coventry CV4 7AL (02476) 574623 J.F.Hanna at warwick.ac.uk From spoel at xray.bmc.uu.se Sat Sep 23 19:14:14 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Sat, 23 Sep 2006 19:14:14 +0200 Subject: [gmx-users] Changing output frequency when doing a continuation with tpbconv In-Reply-To: References: Message-ID: <45156B66.2090905@xray.bmc.uu.se> Joanne Hanna wrote: > Hi > > I was wondering if you can change the output frequency of coordinates written to the *.trr file when you are doing continuation runs using tpbconv. > > grompp -t -e -p -c -f -o > Thanks > Jo > > Joanne Hanna > Department of Chemistry > University of Warwick > Coventry > CV4 7AL > > (02476) 574623 > J.F.Hanna at warwick.ac.uk > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > From chris.neale at utoronto.ca Sat Sep 23 19:27:15 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Sat, 23 Sep 2006 13:27:15 -0400 Subject: [gmx-users] about box size (II) Message-ID: <20060923132715.5jw9j3ba3miso0oo@webmail.utoronto.ca> Appologies, I didn't realize that the sides were unequal. This should work: editconf -f in.gro -o out.gro -d 0.0 -bt triclinic From spoel at xray.bmc.uu.se Sun Sep 24 19:55:40 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Sun, 24 Sep 2006 19:55:40 +0200 Subject: [gmx-users] execution of water tutorial files on BG/L In-Reply-To: <20060920200039.7D95.FUJISAKI@bu.edu> References: <20060920200039.7D95.FUJISAKI@bu.edu> Message-ID: <4516C69C.5020700@xray.bmc.uu.se> Hiroshi Fujisaki wrote: > Dear Gromacs users, > > After installing fftw-3.1.2 and gromacs itself on our > BlueGene facility, I am testing the tutorial > files, but I fail when I try all of them. For example, > for the water case (.../share/gromacs/tutor/water), > "grompp -v" seems to work, but "mdrun -v" suddenly > stops with the following message > "Illegal instruction" Most likely you have compiled for the wrong architecture. > > I've never experienced this when I use gromacs in > a linux machine. Could you suggest something? > The gromacs was compiled with a single precision > and single CPU version. > > I appreciate your help. > > Best wishes, > -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From tsjerkw at gmail.com Mon Sep 25 10:12:22 2006 From: tsjerkw at gmail.com (Tsjerk Wassenaar) Date: Mon, 25 Sep 2006 10:12:22 +0200 Subject: [gmx-users] about box size (II) In-Reply-To: <4514D2DF.0000E7.16859@bj163app78.163.com> References: <4514D2DF.0000E7.16859@bj163app78.163.com> Message-ID: <8ff898150609250112va72d13cs5a6f4667441f805@mail.gmail.com> Hi zzhwise1, What about using a box that will actually fit your system, i.e. 3, 2, 6? Sounds rather intuitive to me. Also, the observation that your system "inverts" has to do with periodic boundary conditions, i.c. having the system centered at one of the box faces. There was a post about this a few days ago. Nothing to worry about (think periodically, or infinitely even). Tsjerk On 9/23/06, zzhwise1 wrote: > thanks chris.neale! > when i change the size to 6.0 (my system is 3,2,6) > ,the upper monolayer turn around ,the bottom to the top ,top to the bottom > ,is it the too big size in the x and y direction? should i to enlarge my > sysytem to (6,6,6) to suit the box size? > thanks! > > > > > > > > > > 3G ? ? ? ? ??? ? ? ? ? ? ? ? ? ? > ? ? ? ? ? 3G ? ? ? ? ? ? ?280 ? ? ? ? ? ? ? ? ? ? ? ? ? > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > -- Tsjerk A. Wassenaar, Ph.D. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 From asaraujo at if.sc.usp.br Mon Sep 25 11:35:54 2006 From: asaraujo at if.sc.usp.br (Alexandre Suman de Araujo) Date: Mon, 25 Sep 2006 09:35:54 +0000 Subject: [gmx-users] Nitrate ion Message-ID: <4517A2FA.2040505@if.sc.usp.br> Hi GMXers I'm trying to use in my simulations the nitrate ion defined in OPLS force field as atom-types opls_787 and opls_788, but when I look at OPLS bonded parameters in ffoplsaabon.itp I can't find bonds, angles or dihedral parameters with it's bond_type (N and O as defined in ffoplsaanb.itp). Are these bond_types correct? If yes, where are the bond parameters for them? Does anybody know the paper where these parameter were published? Thank's -- Alexandre Suman de Araujo asaraujo at if.sc.usp.br UIN: 6194055 IFSC - USP - S?o Carlos - Brasil From chris.neale at utoronto.ca Mon Sep 25 15:24:32 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Mon, 25 Sep 2006 09:24:32 -0400 Subject: [gmx-users] crystal waters crash parallel but not serial Message-ID: <20060925092432.7wp7sog2clwk4ook@webmail.utoronto.ca> My run crashes in parallel but not in serial. I have narrowed it down to the inclusion of crystal waters, but can't imagine what the problem could be that would occur only on parallel. I have done three reps of each situation in order to be sure that it is not a fluke. It's easy enough to take a pass on parallel runs for now, but I am worried about my system and basically I am asking the question: "does anybody know that something like this would only happen if a system is otherwise incorrectly made or could this be a quirk of multiple water groups / ordering of groups / pressure coupling / something else across multiple processors?" My system here is an opls-aa protein in a POPE/DMPE membrane with tip4p waters. Single precision. I am using the double-pairlist inclusion method to scale the lipid 1-4 interactions. It runs fine through initial protein heavy atom position restraints (0.5ns) and then fine again with no topological restraints (3.5ns). When I repeat this setup procedure, this time also with the crystal waters as moleculetype xtip4p.itp/residue XSOL so that I can restrain their positions as well, it runs fine for 0.5ns. However, if I try to repeat this in parallel it crashes after ~40ps. I can extend this time by increasing the number of EM steps or not restraining the crystal waters (worrysome), but still it eventually crashes. I have repeated this 3 times with parallel on 4 procs and 3 times running on single processors. I also did one additional replica in double precision that crashed on parallel (8ps) and ran fine for 500ps on serial. All of my crystal waters and my protein (the only things that are ever restrained) are located on the first processor. I don't use shuffle since I use position restraints. I have ordered the topology Protein, crystal water, membrane, bulk water (and the includes in the same order) and have temperature coupling groups that are 1)protein, 2)lipid, 3)crystal + bulk water. I use lincs. When the run crashes in parallel, the frame prior to the crash shows a single exploding water molecule (bulk water not crystal water). However this was only 2 times (the others gave me a silent compute-forever death even with kill -HUP so I didn't get to see the frame) and the large number of bulk waters means that this might just be by chance. Thanks for any comments. Chris. From quantrum75 at yahoo.com Mon Sep 25 15:42:59 2006 From: quantrum75 at yahoo.com (Rama Gullapalli) Date: Mon, 25 Sep 2006 06:42:59 -0700 (PDT) Subject: [gmx-users] g_rotacf In-Reply-To: Message-ID: <20060925134300.5077.qmail@web31409.mail.mud.yahoo.com> Dear Dr Spoel Thank you for the reply. But I do not quite follow how -noaver does it. I want to compute the P-N vector of lipid molecules and average it over the 128 molecules in the bilayer. Do I make a group containing the numbers of the P and N molecules in a single group ( 256 atoms) and use g_rotacf with -noaver? Will that compute the rotational correlation of the individual P-N vectors of each lipid molecule and average it over 128 molecules? Thanks in advance Regards Rama David van der Spoel wrote: On Fri, 22 Sep 2006, Rama Gullapalli wrote: >Hello everybody, > > I have nearly 100 different vectors to analyse using g_rotacf. I was wondering if there was anyway to do this in GROMACS simultaneously since g_rotacf does not have have the -ng option like in g_traj or others. > -noaver > I would imagine one could use a awk script to run g_rotacf to run a hundred times, but I am not sure how to go about it. If anyone can provide me with pointers on that it would be great > > Thanks in advance > Rama > > >--------------------------------- >Talk is cheap. Use Yahoo! Messenger to make PC-to-Phone calls. Great rates starting at 1?/min. -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php --------------------------------- Talk is cheap. Use Yahoo! Messenger to make PC-to-Phone calls. Great rates starting at 1?/min. -------------- next part -------------- An HTML attachment was scrubbed... URL: From ashkani_2003 at yahoo.com Mon Sep 25 15:55:26 2006 From: ashkani_2003 at yahoo.com (jahanshah ashkani) Date: Mon, 25 Sep 2006 06:55:26 -0700 (PDT) Subject: [gmx-users] How can I remove water and ion molecules Message-ID: <20060925135526.58081.qmail@web50404.mail.yahoo.com> Hi, How can I remove water and ion molecules from the pdb file after energy minimization and molecular dynamic simulation? Thank you very much. Sincerely yours, Jahanshah Ashkani, PhD student of Biotechnology & Genetics, University of the Western Cape, Biotechnology Department, Private Bag X17, 7735 Bellville, Cape Town, South Africa jashkani at mail.biotech.uwc.ac.za --------------------------------- Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From ramorimabreu at gmail.com Mon Sep 25 16:39:14 2006 From: ramorimabreu at gmail.com (Ricardo Amorim) Date: Mon, 25 Sep 2006 11:39:14 -0300 Subject: [gmx-users] gromacs with altix and mpich Message-ID: Hi I have trying to install gromacs-3.3.1 in SGI Altix 3000 machine (running Suse9). Mpich-1.2.7p1 was compiled with the follow parameters: ./configure --with-device=ch_shmem Mpi was tested running NAS benchmark. Serial Gromacs runs with no problem, but parallel not works. Gromacs was compiled with: ./configure --enable-mpi --program-suffix="_mpi_f" --prefix=/usr/local/gromacs make make check make install When I try to run (water example): 1. grompp_mpi_f -np 1 2. mpich -np 1 /usr/local/gromacs/bin/mdrun_mpi_f works, but 1. grompp_mpi_f -np 8 2. mpich -np 8 /usr/local/gromacs/bin/mdrun_mpi_f I receive the message: Child process died unexpectedly from signal 11 /usr/local/mpich/bin/mpirun: line 1: 7656 Aborted /usr/local/gromacs/bin/mdrun_mpi_f Please, someone knows how to solve this problem? Thanks From fujisaki at bu.edu Mon Sep 25 16:52:34 2006 From: fujisaki at bu.edu (Hiroshi Fujisaki) Date: Mon, 25 Sep 2006 10:52:34 -0400 Subject: [gmx-users] execution of water tutorial files on BG/L In-Reply-To: <4516C69C.5020700@xray.bmc.uu.se> References: <20060920200039.7D95.FUJISAKI@bu.edu> <4516C69C.5020700@xray.bmc.uu.se> Message-ID: <20060925104826.7DB0.FUJISAKI@bu.edu> Dear David, THanks for your reply. I noticed what you said, and actually our system at Boston University has a frontend (linux) and a backend (BG/L). http://scv.bu.edu/SCV/Archive/IBM/BGL/GettingStarted.html#COMPILE I seemed to compile gromacs on linux and tried to run it on BG/L (or vice versa?). So my next question is how to solve this problem? Is this a question only administrators can solve? Best wishes, > Hiroshi Fujisaki wrote: > > Dear Gromacs users, > > > > After installing fftw-3.1.2 and gromacs itself on our > > BlueGene facility, I am testing the tutorial > > files, but I fail when I try all of them. For example, > > for the water case (.../share/gromacs/tutor/water), > > "grompp -v" seems to work, but "mdrun -v" suddenly > > stops with the following message > > "Illegal instruction" > > Most likely you have compiled for the wrong architecture. > > > > > I've never experienced this when I use gromacs in > > a linux machine. Could you suggest something? > > The gromacs was compiled with a single precision > > and single CPU version. > > > > I appreciate your help. > > > > Best wishes, > > > > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Hiroshi Fujisaki From vikbajaj at gmail.com Mon Sep 25 17:24:25 2006 From: vikbajaj at gmail.com (Vik Bajaj) Date: Mon, 25 Sep 2006 11:24:25 -0400 Subject: [gmx-users] configuration of system for small molecule crystal simulations Message-ID: <63234d0609250824y127ffc64gc76bf3f7e059cdaf@mail.gmail.com> Hello, I am attempting to simulate a small molecule in an orthorhombic unit cell with z=4; there is no solvent. In this case, the crystal packing forces are largely responsible for the molecular conformation, and therefore the symmetry representation is critical. I have put the molecule in a triclinic box with dimensions equal to the lattice dimensions, and I am not certain that this will result in appropriate boundary conditions. My simulation is currently blowing up, so I am revisiting the initial setup and minimization. If someone can clarify or provide an example of a similar problem, I would appreciate it very much. -Vik From Mark.Abraham at anu.edu.au Mon Sep 25 17:37:43 2006 From: Mark.Abraham at anu.edu.au (Mark Abraham) Date: Tue, 26 Sep 2006 01:37:43 +1000 Subject: [gmx-users] How can I remove water and ion molecules In-Reply-To: <20060925135526.58081.qmail@web50404.mail.yahoo.com> References: <20060925135526.58081.qmail@web50404.mail.yahoo.com> Message-ID: <4517F7C7.5050305@anu.edu.au> jahanshah ashkani wrote: > Hi, > How can I remove water and ion molecules from the pdb file after energy > minimization and molecular dynamic simulation? From a pdb file is easy - just get a text editor and delete those lines. Never mind about the atom or residue numbering. Is this the question you meant to ask? Mark From Florian.Haberl at chemie.uni-erlangen.de Mon Sep 25 18:31:13 2006 From: Florian.Haberl at chemie.uni-erlangen.de (Florian Haberl) Date: Mon, 25 Sep 2006 18:31:13 +0200 Subject: [gmx-users] execution of water tutorial files on BG/L In-Reply-To: <20060925104826.7DB0.FUJISAKI@bu.edu> References: <20060920200039.7D95.FUJISAKI@bu.edu> <4516C69C.5020700@xray.bmc.uu.se> <20060925104826.7DB0.FUJISAKI@bu.edu> Message-ID: <200609251831.14232.Florian.Haberl@chemie.uni-erlangen.de> hi, On Monday 25 September 2006 16:52, Hiroshi Fujisaki wrote: > Dear David, > > THanks for your reply. > I noticed what you said, and actually our system at > Boston University has a frontend (linux) and a backend (BG/L). > http://scv.bu.edu/SCV/Archive/IBM/BGL/GettingStarted.html#COMPILE > > I seemed to compile gromacs on linux and tried to > run it on BG/L (or vice versa?). So my next question is > how to solve this problem? Is this a question only > administrators can solve? You have to crosscompile as your link say, or easier solution you submit an interactive job (don t know if this works with ibm tool but should be) and than you can compile on one node. Else you have to choose correct architecture and compiler as the howto say: with tcsh shell you can try setenv CC blrts_xlc setenv F77 blrts_xlf setenv CXX blrts_xlC all other is an extension from the example: setenv CCFLAGS -O3 -qarch=440 -qtune=440 setenv F77FLAGS -O3 -qarch=440 -qtune=440 setenv CXXFLAGS -O3 -qarch=440 -qtune=440 .. C_LIBS = $(YOUR_C_LIBS) \ -L/bgl/BlueLight/ppcfloor/bglsys/lib \ -lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts C_INCLUDES = -I/bgl/BlueLight/ppcfloor/bglsys/include \ $(YOUR_C_INCLUDES) F77_LIBS = $(YOUR_F77_LIBS) \ -L/bgl/BlueLight/ppcfloor/bglsys/lib \ -lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts F77_INCLUDES = -I/bgl/BlueLight/ppcfloor/bglsys/include \ $(YOUR_F77_INCLUDES) CXX_LIBS = $(YOUR_CXX_LIBS) \ -L/bgl/BlueLight/ppcfloor/bglsys/lib \ -lcxxmpich.rts -lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts CXX_INCLUDES = -I/bgl/BlueLight/ppcfloor/bglsys/include \ $(YOUR_CXX_INCLUDES) Normally it should work, you also have to compile fftw on this architecture. Greetings, Florian > > Best wishes, > > > Hiroshi Fujisaki wrote: > > > Dear Gromacs users, > > > > > > After installing fftw-3.1.2 and gromacs itself on our > > > BlueGene facility, I am testing the tutorial > > > files, but I fail when I try all of them. For example, > > > for the water case (.../share/gromacs/tutor/water), > > > "grompp -v" seems to work, but "mdrun -v" suddenly > > > stops with the following message > > > "Illegal instruction" > > > > Most likely you have compiled for the wrong architecture. > > > > > I've never experienced this when I use gromacs in > > > a linux machine. Could you suggest something? > > > The gromacs was compiled with a single precision > > > and single CPU version. > > > > > > I appreciate your help. > > > > > > Best wishes, > > > > -- > > David. > > ________________________________________________________________________ > > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > > Dept. of Cell and Molecular Biology, Uppsala University. > > Husargatan 3, Box 596, 75124 Uppsala, Sweden > > phone: 46 18 471 4205 fax: 46 18 511 755 > > spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > _______________________________________________ > > gmx-users mailing list gmx-users at gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-request at gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) ? 9131 ? 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- From wjallen at vt.edu Mon Sep 25 19:04:43 2006 From: wjallen at vt.edu (wjallen at vt.edu) Date: Mon, 25 Sep 2006 13:04:43 -0400 Subject: [gmx-users] Covalent bonds between topology files Message-ID: <1159203883.45180c2bc280c@webmail.vt.edu> Hello fellow gromacs users, I am working with a protein that has an FAD cofactor that is covalently bound to a specific residue. I am trying to model the protein in a style similar to Dr. John E. Kerrigan's drug tutorial. I used pdb2gmx to create topology and coordinate files for the protein, and the Dundee PRODRG server to create a topology and coordinates (.gro) for the FAD molecule. I physically combined the coordinate files, and I included the topology of the FAD molecule in the header of the protein topology file: ; Include chain topologies #include "protein.itp" #include "FAD.itp" and I included the FAD molecule at the end of the file: [ molecules ] ; Compound #mols Protein 1 FAD 1 Everything has been working well, the whole structure can be minimized and processed so I know I have not made any errors yet. But, this is where I am stuck. I need to covalently bind an atom in the FAD molecule to a residue in the protein chain before I start minimizing anything. Any suggestions on how to approach this would be greatly appreciated! Cheers, W. Allen From kia.balali-mood at bioch.ox.ac.uk Mon Sep 25 18:23:48 2006 From: kia.balali-mood at bioch.ox.ac.uk (Kia Balali-Mood) Date: Mon, 25 Sep 2006 17:23:48 +0100 Subject: [gmx-users] How can I remove water and ion molecules In-Reply-To: <20060925153742.CEA672407F@xray.bmc.uu.se> Message-ID: <20060925162348.B786453081@webmail219.herald.ox.ac.uk> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From gportel at gwdg.de Mon Sep 25 17:05:40 2006 From: gportel at gwdg.de (Guillem Portella) Date: Mon, 25 Sep 2006 17:05:40 +0200 Subject: [gmx-users] How can I remove water and ion molecules In-Reply-To: <20060925135526.58081.qmail@web50404.mail.yahoo.com> References: <20060925135526.58081.qmail@web50404.mail.yahoo.com> Message-ID: <200609251705.40637.gportel@gwdg.de> man grep with special attention to -v option bounus ball: it also works before em and md Cheers On Monday 25 September 2006 15:55, jahanshah ashkani wrote: > Hi, > How can I remove water and ion molecules from the pdb file after energy > minimization and molecular dynamic simulation? Thank you very much. > > Sincerely yours, > > > Jahanshah Ashkani, > PhD student of Biotechnology & Genetics, > University of the Western Cape, > Biotechnology Department, > Private Bag X17, > 7735 Bellville, > Cape Town, > South Africa > jashkani at mail.biotech.uwc.ac.za > > --------------------------------- > Do you Yahoo!? > Everyone is raving about the all-new Yahoo! Mail. -- *************************************************************** Guillem Portella Computational biomolecular dynamics group at the Max Planck Institute for Biophysical Chemistry Am Fassberg 11 D-37077 Goettingen -- Germany -- phone: ++49-551-2012309 fax: ++49-551-2012302 Email: gportel at gwdg.de webpage:http://www.mpibpc.mpg.de/groups/grubmueller/start/people/gportel/index.php *************************************************************** From zhoumadison at gmail.com Mon Sep 25 22:14:50 2006 From: zhoumadison at gmail.com (Lei Zhou) Date: Mon, 25 Sep 2006 16:14:50 -0400 Subject: [gmx-users] Extracting C-alpha component from all-atom Hessian matrix In-Reply-To: References: Message-ID: Dear GMX-users, I have been working on extracting the C-alpha component from the all-atom Hessian matrix, according to the equation proposed initially by Berk, H'=Hxx-HxyHyy-1Hyx. It worked quite nice in my hand and for a test protein, there is almost no visual difference in the confromational changes described by the eigenvectors between two methods (all-atom normal mode or C-alpha only). I am wondering whether there is a reference for this equation? Is it based on Gram-Schmidt formula for deriving a new set of vectors? There was a old paper by Brooks and Karplus (J. Comp. Chem., 1995) gave a detailed description of the normal mode analysis and prosposed a methods for extracting dihedral angle normal modes. So is there any difference between the method they proposed and equation mentioned above? Thank you for the help. Lei Zhou Columbia University [gmx-users] Normal Mode Analysis on Calphas only ?? *Berk Hess* gmx3 at hotmail.com *Wed May 18 08:42:23 CEST 2005* - Previous message: [gmx-users] Normal Mode Analysis on Calphas only ?? - Next message: [gmx-users] Normal Mode Analysis on Calphas only ?? - *Messages sorted by:* [ date ] [ thread ] [ subject ] [ author ] ------------------------------ Here is the formula (thanks to Herman Berendsen). I was slightly wrong. You first need to reduce the Hessian and then diagonalize the C-alpha only Hessian. definitions: Interesting particle coordinates: x Uninsteresting particle coordinates y full hessian in terms of (x, y): H Split H into four blocks: Hxx Hxy H = Hyx Hyy Then the hessian H' in the subspace of x coordinates, under the condition that the y coordinates are in a minimum, is H' = Hxx - Hxy Hyy^-1 Hyx This is a simple transformation, requiring only one inversion and two matrix multiplications. Berk. -------------- next part -------------- An HTML attachment was scrubbed... URL: From quantrum75 at yahoo.com Mon Sep 25 22:27:11 2006 From: quantrum75 at yahoo.com (Rama Gullapalli) Date: Mon, 25 Sep 2006 13:27:11 -0700 (PDT) Subject: [gmx-users] g_rotacf In-Reply-To: <20060925134300.5077.qmail@web31409.mail.mud.yahoo.com> Message-ID: <20060925202711.65453.qmail@web31412.mail.mud.yahoo.com> Dear Dr Spoel Sorry for the earlier hasty mail. I figured out how the -noaver option works. Thanks Sincerely Regards Rama Rama Gullapalli wrote: Dear Dr Spoel Thank you for the reply. But I do not quite follow how -noaver does it. I want to compute the P-N vector of lipid molecules and average it over the 128 molecules in the bilayer. Do I make a group containing the numbers of the P and N molecules in a single group ( 256 atoms) and use g_rotacf with -noaver? Will that compute the rotational correlation of the individual P-N vectors of each lipid molecule and average it over 128 molecules? Thanks in advance Regards Rama David van der Spoel wrote: On Fri, 22 Sep 2006, Rama Gullapalli wrote: >Hello everybody, > > I have nearly 100 different vectors to analyse using g_rotacf. I was wondering if there was anyway to do this in GROMACS simultaneously since g_rotacf does not have have the -ng option like in g_traj or others. > -noaver > I would imagine one could use a awk script to run g_rotacf to run a hundred times, but I am not sure how to go about it. If anyone can provide me with pointers on that it would be great > > Thanks in advance > Rama > > >--------------------------------- >Talk is cheap. Use Yahoo! Messenger to make PC-to-Phone calls. Great rates starting at 1?/min. -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php --------------------------------- Talk is cheap. Use Yahoo! Messenger to make PC-to-Phone calls. Great rates starting at 1?/min._______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php --------------------------------- Talk is cheap. Use Yahoo! Messenger to make PC-to-Phone calls. Great rates starting at 1?/min. -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.groenhof at rug.nl Mon Sep 25 21:44:02 2006 From: g.groenhof at rug.nl (Gerrit Groenhof) Date: Mon, 25 Sep 2006 21:44:02 +0200 Subject: [gmx-users] How can I remove water and ion molecules In-Reply-To: <200609251705.40637.gportel@gwdg.de> References: <20060925135526.58081.qmail@web50404.mail.yahoo.com> <200609251705.40637.gportel@gwdg.de> Message-ID: <3e4ed3af16738b57af07a21dc385d2e2@rug.nl> make an index file entry with the stuff you want to write in your pdb, and use editconf -n to dump only that. On Sep 25, 2006, at 5:05 PM, Guillem Portella wrote: > > man grep > > with special attention to -v option > > bounus ball: it also works before em and md > > Cheers > > > On Monday 25 September 2006 15:55, jahanshah ashkani wrote: >> Hi, >> How can I remove water and ion molecules from the pdb file after >> energy >> minimization and molecular dynamic simulation? Thank you very much. >> >> Sincerely yours, >> >> >> Jahanshah Ashkani, >> PhD student of Biotechnology & Genetics, >> University of the Western Cape, >> Biotechnology Department, >> Private Bag X17, >> 7735 Bellville, >> Cape Town, >> South Africa >> jashkani at mail.biotech.uwc.ac.za >> >> --------------------------------- >> Do you Yahoo!? >> Everyone is raving about the all-new Yahoo! Mail. > > -- > *************************************************************** > Guillem Portella > Computational biomolecular dynamics group at the > Max Planck Institute for Biophysical Chemistry > Am Fassberg 11 > D-37077 Goettingen -- Germany -- > phone: ++49-551-2012309 > fax: ++49-551-2012302 > Email: gportel at gwdg.de > > webpage:http://www.mpibpc.mpg.de/groups/grubmueller/start/people/ > gportel/index.php > *************************************************************** > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > Note, from 2005 on my email adress has changed to ggroenh at gwdg.de From fujisaki at bu.edu Tue Sep 26 00:48:21 2006 From: fujisaki at bu.edu (Hiroshi Fujisaki) Date: Mon, 25 Sep 2006 18:48:21 -0400 Subject: [gmx-users] execution of water tutorial files on BG/L In-Reply-To: <200609251831.14232.Florian.Haberl@chemie.uni-erlangen.de> References: <20060925104826.7DB0.FUJISAKI@bu.edu> <200609251831.14232.Florian.Haberl@chemie.uni-erlangen.de> Message-ID: <20060925184520.7DBF.FUJISAKI@bu.edu> Dear Florian, Our administrator is now trying to compile gromacs on BlueGene, but he now fails. I attach the error make log below. I appreciate your comments. ############################################################## Making all in include make[1]: Entering directory `/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/incl ude' Making all in . make[2]: Entering directory `/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/incl ude' make[2]: Nothing to be done for `all-am'. make[2]: Leaving directory `/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/inclu de' Making all in types make[2]: Entering directory `/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/incl ude/types' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/inclu de/types' make[1]: Leaving directory `/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/inclu de' Making all in src make[1]: Entering directory `/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/src' make all-recursive make[2]: Entering directory `/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/src' Making all in gmxlib make[3]: Entering directory `/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/src/ gmxlib' Making all in nonbonded make[4]: Entering directory `/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/src/ gmxlib/nonbonded' Making all in nb_kernel make[5]: Entering directory `/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/src/ gmxlib/nonbonded/nb_kernel' blrts_xlc -DHAVE_CONFIG_H -I. -I. -I../../../../src -c -o mknb.o mknb.c blrts_xlc -DHAVE_CONFIG_H -I. -I. -I../../../../src -c -o mknb_metacode.o mknb_m etacode.c blrts_xlc -DHAVE_CONFIG_H -I. -I. -I../../../../src -c -o mknb_common.o mknb_com mon.c blrts_xlc -DHAVE_CONFIG_H -I. -I. -I../../../../src -c -o mknb_declarations.o mk nb_declarations.c blrts_xlc -DHAVE_CONFIG_H -I. -I. -I../../../../src -c -o mknb_outerloop.o mknb_ outerloop.c blrts_xlc -DHAVE_CONFIG_H -I. -I. -I../../../../src -c -o mknb_innerloop.o mknb_ innerloop.c blrts_xlc -DHAVE_CONFIG_H -I. -I. -I../../../../src -c -o mknb_interactions.o mk nb_interactions.c blrts_xlc -DHAVE_CONFIG_H -I. -I. -I../../../../src -o mknb mknb.o mknb_metacode .o mknb_common.o mknb_declarations.o mknb_outerloop.o mknb_innerloop.o mknb_inte ractions.o rm -f kernel-stamp ./mknb -double -software_invsqrt >>> Gromacs nonbonded kernel generator (-h for help) >>> Generating double precision functions in C. >>> Using Gromacs software version of 1/sqrt(x). Error: Cannot open nb_kernel010_c.c for writing. make[5]: *** [kernel-stamp] Error 1 make[5]: Leaving directory `/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/src/g mxlib/nonbonded/nb_kernel' make[4]: *** [all-recursive] Error 1 make[4]: Leaving directory `/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/src/g mxlib/nonbonded' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/src/g mxlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/src' make: *** [all-recursive] Error 1 ############################################################# > hi, > > On Monday 25 September 2006 16:52, Hiroshi Fujisaki wrote: > > Dear David, > > > > THanks for your reply. > > I noticed what you said, and actually our system at > > Boston University has a frontend (linux) and a backend (BG/L). > > http://scv.bu.edu/SCV/Archive/IBM/BGL/GettingStarted.html#COMPILE > > > > I seemed to compile gromacs on linux and tried to > > run it on BG/L (or vice versa?). So my next question is > > how to solve this problem? Is this a question only > > administrators can solve? > > You have to crosscompile as your link say, or easier solution you submit an > interactive job (don t know if this works with ibm tool but should be) and > than you can compile on one node. > > Else you have to choose correct architecture and compiler as the howto say: > > with tcsh shell you can try > > setenv CC blrts_xlc > setenv F77 blrts_xlf > setenv CXX blrts_xlC > > all other is an extension from the example: > > setenv CCFLAGS -O3 -qarch=440 -qtune=440 > setenv F77FLAGS -O3 -qarch=440 -qtune=440 > setenv CXXFLAGS -O3 -qarch=440 -qtune=440 > .. > > > C_LIBS = $(YOUR_C_LIBS) \ > -L/bgl/BlueLight/ppcfloor/bglsys/lib \ > -lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts > > C_INCLUDES = -I/bgl/BlueLight/ppcfloor/bglsys/include \ > $(YOUR_C_INCLUDES) > > F77_LIBS = $(YOUR_F77_LIBS) \ > -L/bgl/BlueLight/ppcfloor/bglsys/lib \ > -lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts > > F77_INCLUDES = -I/bgl/BlueLight/ppcfloor/bglsys/include \ > $(YOUR_F77_INCLUDES) > > CXX_LIBS = $(YOUR_CXX_LIBS) \ > -L/bgl/BlueLight/ppcfloor/bglsys/lib \ > -lcxxmpich.rts -lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts > > CXX_INCLUDES = -I/bgl/BlueLight/ppcfloor/bglsys/include \ > $(YOUR_CXX_INCLUDES) > > > Normally it should work, you also have to compile fftw on this architecture. > > > Greetings, > > Florian > > > > > > Best wishes, > > > > > Hiroshi Fujisaki wrote: > > > > Dear Gromacs users, > > > > > > > > After installing fftw-3.1.2 and gromacs itself on our > > > > BlueGene facility, I am testing the tutorial > > > > files, but I fail when I try all of them. For example, > > > > for the water case (.../share/gromacs/tutor/water), > > > > "grompp -v" seems to work, but "mdrun -v" suddenly > > > > stops with the following message > > > > "Illegal instruction" > > > > > > Most likely you have compiled for the wrong architecture. > > > > > > > I've never experienced this when I use gromacs in > > > > a linux machine. Could you suggest something? > > > > The gromacs was compiled with a single precision > > > > and single CPU version. > > > > > > > > I appreciate your help. > > > > > > > > Best wishes, > > > > > > -- > > > David. > > > ________________________________________________________________________ > > > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > > > Dept. of Cell and Molecular Biology, Uppsala University. > > > Husargatan 3, Box 596, 75124 Uppsala, Sweden > > > phone: 46 18 471 4205 fax: 46 18 511 755 > > > spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se > > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > > _______________________________________________ > > > gmx-users mailing list gmx-users at gromacs.org > > > http://www.gromacs.org/mailman/listinfo/gmx-users > > > Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to gmx-users-request at gromacs.org. > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > ------------------------------------------------------------------------------- > Florian Haberl > Computer-Chemie-Centrum > Universitaet Erlangen/ Nuernberg > Naegelsbachstr 25 > D-91052 Erlangen > Telephone: +49(0) $BchC(B9131 $BchC(B85 26581 > Mailto: florian.haberl AT chemie.uni-erlangen.de > ------------------------------------------------------------------------------- > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Hiroshi Fujisaki From Mark.Abraham at anu.edu.au Tue Sep 26 02:08:29 2006 From: Mark.Abraham at anu.edu.au (Mark Abraham) Date: Tue, 26 Sep 2006 10:08:29 +1000 Subject: [gmx-users] Covalent bonds between topology files In-Reply-To: <1159203883.45180c2bc280c@webmail.vt.edu> References: <1159203883.45180c2bc280c@webmail.vt.edu> Message-ID: <45186F7D.6040604@anu.edu.au> wjallen at vt.edu wrote: > Everything has been working well, the whole structure can be minimized and > processed so I know I have not made any errors yet. But, this is where I am > stuck. I need to covalently bind an atom in the FAD molecule to a residue in > the protein chain before I start minimizing anything. Any suggestions on how > to approach this would be greatly appreciated! All atoms involved in bonded interactions must be defined within the same [ molecule ] segment. Thus you will need to go back and generate a [ molecule ] segment that has this, and the atoms numbered correctly (so you can't just concatenate). Mark From zzhwise1 at 163.com Tue Sep 26 04:40:48 2006 From: zzhwise1 at 163.com (zzhwise1) Date: Tue, 26 Sep 2006 10:40:48 +0800 (CST) Subject: [gmx-users] about box size (III) Message-ID: <45189330.000037.01198@bj163app88.163.com> hi everyone since i met the problem several days ago,mang good friends help me !i thank them very much! and now,i explicit my problem and the solution ditailly,hope to help who will meet the same problem! my system is composed of two opesite monolayers,and the size is 3,2,6 in x,y ,z directions,first i set the box size 6x6x6,but the upper inverted,the i took the solution that provied by good friend chris.neale,i uesd the editconf option,-f input.gro -o output.gro -bt triclinic -box 4 4 6 .just as that ! and ,my file can go smoothly! thanks chris very much! -------------- next part -------------- An HTML attachment was scrubbed... URL: From anwar at cdfd.org.in Tue Sep 26 12:58:52 2006 From: anwar at cdfd.org.in (anwar at cdfd.org.in) Date: Tue, 26 Sep 2006 03:58:52 -0700 (PDT) Subject: [gmx-users] water molecules in vacuum simulation. Message-ID: <4684156.1159238767765.JavaMail.nobody@sunserver> Dear users, Is it possible to perform an invacuum simulation with few constrained water molecules? I dont want to use the explicit solvent, but want to use the crystallographic water molecules in protein and perform invacuum simulation. regards Anwar ---------------------- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 anwar.m1 at gmail.com ----------------------- - From chris.neale at utoronto.ca Tue Sep 26 08:17:08 2006 From: chris.neale at utoronto.ca (chris.neale at utoronto.ca) Date: Tue, 26 Sep 2006 02:17:08 -0400 Subject: [gmx-users] about box size (III) Message-ID: <20060926021708.380p0cn5obcc0gg8@webmail.utoronto.ca> editconf option,-f input.gro -o output.gro -bt triclinic -box 4 4 6 is not recommended for a box size of size is 3,2,6 in x,y,z use -d 0.0 instead of -box 4 4 6 Read about it here: http://www.gromacs.org/documentation/reference/online/editconf.html I am assuming that you are using periodic boundary conditions and pressure scaling. In that case -box 4 4 6 will probably be fine, but be sure to visualize your system (you could use VMD). If you are unsure about periodicity (Tsjerk recently pointed out that what looks incorrect may in fact be correct) then I urge you to turn on the periodic representation in VMD and look at the system in this manner. Chris. From ninoomani at yahoo.co.in Tue Sep 26 09:44:57 2006 From: ninoomani at yahoo.co.in (ninoo mani) Date: Tue, 26 Sep 2006 08:44:57 +0100 (BST) Subject: [gmx-users] g_rms, matrix and raw data Message-ID: <20060926074457.34792.qmail@web8802.mail.in.yahoo.com> Dear all I run g_rms with -m option that produces a matrix in .xpm format. Is it possible somehow to obtain raw data i.e. the real numerical values of the elements of the matrix? Thanking in advance, Ninoo __________________________________________________________ Yahoo! India Answers: Share what you know. Learn something new http://in.answers.yahoo.com/ From tsjerkw at gmail.com Tue Sep 26 10:07:06 2006 From: tsjerkw at gmail.com (Tsjerk Wassenaar) Date: Tue, 26 Sep 2006 10:07:06 +0200 Subject: [gmx-users] configuration of system for small molecule crystal simulations In-Reply-To: <63234d0609250824y127ffc64gc76bf3f7e059cdaf@mail.gmail.com> References: <63234d0609250824y127ffc64gc76bf3f7e059cdaf@mail.gmail.com> Message-ID: <8ff898150609260107t6f88ab1dhc8be1d74e313ca49@mail.gmail.com> Hi Vik, Did you make sure the (rotational) orientation of your molecule corresponded to the triclinic unit cell? And did you visualize the crystal (using e.g. genconf to extend the system)? Hope it helps, Tsjerk On 9/25/06, Vik Bajaj wrote: > Hello, > > I am attempting to simulate a small molecule in an orthorhombic unit > cell with z=4; there is no solvent. In this case, the crystal > packing forces are largely responsible for the molecular conformation, > and therefore the symmetry representation is critical. I have put the > molecule in a triclinic box with dimensions equal to the lattice > dimensions, and I am not certain that this will result in appropriate > boundary conditions. My simulation is currently blowing up, so I am > revisiting the initial setup and minimization. > > If someone can clarify or provide an example of a similar problem, I > would appreciate it very much. > > -Vik > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 From priyankaps4 at yahoo.com Tue Sep 26 10:51:50 2006 From: priyankaps4 at yahoo.com (priyanka srivastava) Date: Tue, 26 Sep 2006 01:51:50 -0700 (PDT) Subject: [gmx-users] surface tension Message-ID: <20060926085150.24451.qmail@web39209.mail.mud.yahoo.com> Dear all, what is the unit of surface tension in gromacs analysis? Is it dyn/cm or N/m. As according to me it is coming out to be in terms of N/m but it is attached with a conversion factor of some powers of 10. Kindly guide me. If I am getting e.g. 930.002 as the surface tension then what are it's units? regards, Pri... __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From mark.abraham at anu.edu.au Tue Sep 26 11:03:54 2006 From: mark.abraham at anu.edu.au (Mark Abraham) Date: Tue, 26 Sep 2006 19:03:54 +1000 (EST) Subject: [gmx-users] g_rms, matrix and raw data In-Reply-To: <20060926074457.34792.qmail@web8802.mail.in.yahoo.com> References: <20060926074457.34792.qmail@web8802.mail.in.yahoo.com> Message-ID: <44375.150.101.115.79.1159261434.squirrel@sqmail.anu.edu.au> > Dear all > > I run g_rms with -m option that produces a matrix in > .xpm format. Is it possible somehow to obtain raw data > i.e. the real numerical values of the elements of the > matrix? man g_rms Mark From mark.abraham at anu.edu.au Tue Sep 26 11:13:14 2006 From: mark.abraham at anu.edu.au (Mark Abraham) Date: Tue, 26 Sep 2006 19:13:14 +1000 (EST) Subject: [gmx-users] surface tension In-Reply-To: <20060926085150.24451.qmail@web39209.mail.mud.yahoo.com> References: <20060926085150.24451.qmail@web39209.mail.mud.yahoo.com> Message-ID: <35575.150.101.115.79.1159261994.squirrel@sqmail.anu.edu.au> > Dear all, > > what is the unit of surface tension in gromacs > analysis? Is it dyn/cm or N/m. As according to me it > is coming out to be in terms of N/m but it is attached > with a conversion factor of some powers of 10. > Kindly guide me. If I am getting e.g. 930.002 as the > surface tension then what are it's units? See section 2.2 of the manual. Surface tension isn't actually defined, but after you read that, you'll know which it is. Mark From swolf at bph.rub.de Tue Sep 26 12:10:44 2006 From: swolf at bph.rub.de (Steffen Wolf) Date: Tue, 26 Sep 2006 12:10:44 +0200 Subject: [gmx-users] water molecules in vacuum simulation. In-Reply-To: <4684156.1159238767765.JavaMail.nobody@sunserver> References: <4684156.1159238767765.JavaMail.nobody@sunserver> Message-ID: <4518FCA4.1080305@bph.rub.de> Hi Anwar, the answer is: Yes, sure. CU Steffen > Dear users, > Is it possible to perform an invacuum simulation with few constrained water > molecules? I dont want to use the explicit solvent, but want to use the > crystallographic water molecules in protein and perform invacuum simulation. > regards > Anwar > > ---------------------- > Mohd Anwaruddin > Project Assistant > C/o DR.H.A.Nagarajaram > Lab of Computational Biology and Bioinformatics > Center for DNA Fingerprinting and Diagnostics(CDFD) > Nacharam > Hyderabad-500 076 > INDIA. > Tel: +91-8413-235467,68,69,70 ext 2019 > anwar.m1 at gmail.com > ----------------------- > > > > - > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Dipl.-Chem. Steffen Wolf Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: swolf at bph.rub.de Web: http://www.bph.rub.de From s.yefimov at rug.nl Tue Sep 26 11:01:45 2006 From: s.yefimov at rug.nl (Serge Yefimov) Date: Tue, 26 Sep 2006 11:01:45 +0200 Subject: [gmx-users] surface tension In-Reply-To: <20060926085150.24451.qmail@web39209.mail.mud.yahoo.com> References: <20060926085150.24451.qmail@web39209.mail.mud.yahoo.com> Message-ID: <4518EC79.3030407@rug.nl> Hi Pri, Surface tension of 930.002 in gromacs units = 93.0002 mN/m or (dyn/cm) serge priyanka srivastava wrote: > Dear all, > > what is the unit of surface tension in gromacs > analysis? Is it dyn/cm or N/m. As according to me it > is coming out to be in terms of N/m but it is attached > with a conversion factor of some powers of 10. > Kindly guide me. If I am getting e.g. 930.002 as the > surface tension then what are it's units? > > regards, > Pri... From vechism at netscape.net Tue Sep 26 15:22:46 2006 From: vechism at netscape.net (vechism at netscape.net) Date: Tue, 26 Sep 2006 09:22:46 -0400 Subject: [gmx-users] EM problem with OPLS and TIP4P In-Reply-To: <20060920212823.nln50eq0gr48c4kg@webmail.utoronto.ca> References: <20060920212823.nln50eq0gr48c4kg@webmail.utoronto.ca> Message-ID: <8C8AF85FDD3E3A3-1784-373B@FWM-M35.sysops.aol.com> -----Original Message----- From: chris.neale at utoronto.ca To: gmx-users at gromacs.org Sent: Wed, 20 Sep 2006 10:28 PM Subject: [gmx-users] EM problem with OPLS and TIP4P Try this: unconstrained_start = no Also ensure that your .top file is correct. Also take a look at your starting positions, where is MW? Also ensure that your waters have the correct order: eg. 871SOL OW 3496 1.935 2.093 1.901 871SOL HW1 3497 1.902 2.172 1.945 871SOL HW2 3498 1.990 2.126 1.830 871SOL MW 3499 1.938 2.107 1.898 The problema was here. In my old tip4p.itp file the water sites were in reverse order. I just change the order and it works now. Thanks. Also try outputting coords for step 20,21,22,23 in the first system and see what is actually happening. _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ________________________________________________________________________ Check Out the new free AIM(R) Mail -- 2 GB of storage and industry-leading spam and email virus protection. -------------- next part -------------- An HTML attachment was scrubbed... URL: From MichaelOwen at creighton.edu Tue Sep 26 17:59:08 2006 From: MichaelOwen at creighton.edu (Owen, Michael) Date: Tue, 26 Sep 2006 10:59:08 -0500 Subject: [gmx-users] VAL group Message-ID: <80C4D42673F70F4B9333B9F3AFFCC5081D8823@EXBE06.blue.jays.creighton.edu> Hello fellow gmx users, when I convert a pdb file of a peptide that contains a valyl residue into a .gro file a separate "group" is made for the atoms in the valyl residue. This has happened when OPLSAA/l and the GROMOS96 53a6 force fields were used. The molecule appears as one in the topology file, and the atomic description of the valyl residue in the pdb file matches that of the ffoplsa.rtp file. An excert from the topology file that shows the structure contains one peptide is below. [ system ] ; Name Protein in water [ molecules ] ; Compound #mols Protein 1 SOL 6973 An excerpt from my index file that shows the VAL group, with 16 atoms that are separated from the protein is below: 28125 28126 28127 28128 28129 28130 28131 28132 28133 28134 28135 28136 28137 28138 28139 28140 28141 28142 28143 28144 28145 28146 28147 28148 28149 28150 28151 28152 28153 28154 28155 28156 28157 28158 28159 28160 28161 28162 [ VAL ] 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 [ SOL ] 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 Could something be wrong with the pdb2gmx program? Thank you in advance for any suggestions. Sincerely, Michael Owen -------------- next part -------------- An HTML attachment was scrubbed... URL: From MichaelOwen at creighton.edu Tue Sep 26 18:10:15 2006 From: MichaelOwen at creighton.edu (Owen, Michael) Date: Tue, 26 Sep 2006 11:10:15 -0500 Subject: [gmx-users] distance restraints: -merge Message-ID: <80C4D42673F70F4B9333B9F3AFFCC5081D8824@EXBE06.blue.jays.creighton.edu> Fellow gmx-users, I would like to constrain the distance of an ion to specific atoms of a protein. I recently read a message in which the use of the option -merge in the pdb2gmx program was suggested. How can I use this option to form these constraints? Thank you for your assistance, Michael Owen -------------- next part -------------- An HTML attachment was scrubbed... URL: From jf163201 at ohiou.edu Tue Sep 26 18:18:53 2006 From: jf163201 at ohiou.edu (Jim Fonseca) Date: Tue, 26 Sep 2006 12:18:53 -0400 Subject: [gmx-users] Which POPC Bilayer to start? In-Reply-To: <000d01c6dcfe$8eab1b20$8aa74a82@Plasma> References: <000d01c6dcfe$8eab1b20$8aa74a82@Plasma> Message-ID: <70FB90EC-756C-4B1E-BBCB-6AA4DD993F3F@ohiou.edu> I've had success with Tieleman's lipids. I used popc128b.pdb. Since it has the extra ns of equilibration, I figured it would cause fewer problems. However, once you start messing around with making hole in the membrane and adding a protein, you'll need to re-equilibrate again (EM & PR). Jim On Sep 20, 2006, at 5:48 PM, Akshay Patny wrote: > Hi All > > I am trying to use POPC bilayer for doing GPCR simulation. > > I have come across two options of generating a POPC bilayer >>>> > > 1. I can generate a POPC bilayer from the VMD Membrane plug-in, > wherein the > membrane is generated from the pre-built membrane square patches > and lipid > tails are (almost) fully extended. > 2. Alternatively, I can download the pre-equilibrated POPC bilayer > from Dr. > Tieleman's website, http://moose.bio.ucalgary.ca/index.php?page=People > > Since, I am new to the GPCR-membrane modeling, can you suggest me > which out > of the above two options can be a better starting point for the > simulation > of my GPCR protein? A membrane generated from VMD or a pre- > equilibrated > membrane?? Would the equilibration time for my protein be lesser in > one out > of the two? > > If option 2 is a good idea then out of popc128a.pdb and > popc128b.pdb (both > available from Prof. Tieleman's website), which will be a better > model to > start with? > > Thank you very much in advance. > Akshay > > Akshay Patny > > Graduate Research Assistant > Faser Hall 417, Department of Medicinal Chemistry > Research Institute of Pharmaceutical Sciences > University of Mississippi > University, MS 38677 > E-mail: akshay17 at olemiss.edu > Tel: 662-915-1286 (office); Web: www.olemiss.edu > > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sridharfirst at gmail.com Tue Sep 26 19:03:10 2006 From: sridharfirst at gmail.com (Sridhar Acharya) Date: Tue, 26 Sep 2006 22:33:10 +0530 Subject: [gmx-users] Problem reading large file in g_covar Message-ID: <45195D4E.505@gmail.com> Hello, I am running g_covar compiled on a sun4 architechture system running solaris 9. But the program halts with the error message that the given xtc file was not found. In fact the xtc file which is 7.1GB was very much existing. I suppose that it is a case of large file. I compiled GROMACS3.1.4 with --enable-largefile. But still the same error occurs. How to make g_covar recognise this file? ########################################################################## :-) G R O M A C S (-: GRoups of Organic Molecules in ACtion for Science :-) VERSION 3.1.4 (-: Copyright (c) 1991-2002, University of Groningen, The Netherlands This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) /users/sridhar/bin/GROMACS314_SOLARIS/SERIAL/sparc-sun-solaris2.9/ultrasparc3/bin/g_covar (-: Option Filename Type Description ------------------------------------------------------------ -f 50NS_WT.xtc Input Generic trajectory: xtc trr trj gro g96 pdb -s ../FILES/b4md_1cyp_WT.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb -n ../FILES/pr_1cyp_WT.ndx Input, Opt! Index file -o eigenval_WT.xvg Output xvgr/xmgr file -v eigenvec_WT.trr Output Full precision trajectory: trr trj -av average_WT.pdb Output Generic structure: gro g96 pdb -l covar_WT.log Output Log file -xpm covar.xpm Output, Opt. X PixMap compatible matrix file -xpma covara.xpm Output, Opt. X PixMap compatible matrix file Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -nice int 0 Set the nicelevel -b time 12000 First frame (ps) to read from trajectory -e time 50000 Last frame (ps) to read from trajectory -dt time -1 Only use frame when t MOD dt = first time (ps) -tu enum ps Time unit: ps, fs, ns, us, ms, s, m or h -[no]fit bool yes Fit to a reference structure -[no]ref bool no Use the deviation from the conformation in the structure file instead of from the average -[no]mwa bool no Mass-weighted covariance analysis -last int -1 Last eigenvector to write away (-1 is till the last) Reading file ../FILES/b4md_1cyp_WT.tpr, VERSION 3.1.4 (single precision) Reading file ../FILES/b4md_1cyp_WT.tpr, VERSION 3.1.4 (single precision) Choose a group for the least squares fit Group 0 ( System) has 41820 elements Group 1 ( Protein) has 4858 elements Group 2 ( Protein-H) has 3775 elements Group 3 ( C-alpha) has 478 elements Group 4 ( Backbone) has 1434 elements Group 5 ( MainChain) has 1913 elements Group 6 (MainChain+Cb) has 2361 elements Group 7 ( MainChain+H) has 2363 elements Group 8 ( SideChain) has 2495 elements Group 9 ( SideChain-H) has 1862 elements Group 10 ( Prot-Masses) has 4858 elements Group 11 ( Non-Protein) has 36962 elements Group 12 ( HEME) has 47 elements Group 13 ( SOL) has 36912 elements Group 14 ( CL-) has 3 elements Group 15 ( Other) has 36962 elements Group 16 (Protein_HEME) has 4905 elements Group 17 (Protein_HEME_CL-) has 4908 elements Select a group: 3 Choose a group for the covariance analysis Group 0 ( System) has 41820 elements Group 1 ( Protein) has 4858 elements Group 2 ( Protein-H) has 3775 elements Group 3 ( C-alpha) has 478 elements Group 4 ( Backbone) has 1434 elements Group 5 ( MainChain) has 1913 elements Group 6 (MainChain+Cb) has 2361 elements Group 7 ( MainChain+H) has 2363 elements Group 8 ( SideChain) has 2495 elements Group 9 ( SideChain-H) has 1862 elements Group 10 ( Prot-Masses) has 4858 elements Group 11 ( Non-Protein) has 36962 elements Group 12 ( HEME) has 47 elements Group 13 ( SOL) has 36912 elements Group 14 ( CL-) has 3 elements Group 15 ( Other) has 36962 elements Group 16 (Protein_HEME) has 4905 elements Group 17 (Protein_HEME_CL-) has 4908 elements Select a group: 3 Note: the fit and analysis group are identical, while the fit is mass weighted and the analysis is not. Making the fit non mass weighted. Constructing covariance matrix (1434x1434)... Fatal error: File 50NS_WT.xtc not found ################################################################################# -- Sridhar Acharya, M Senior Research Fellow Lab of Computational Biology CDFD, Gandipet Campus Hyderabad. AP. INDIA http://www.cdfd.org.in email: sridhar at cdfd.org.in sridharfirst at gmail.com sridharacharya at indiatimes.com Phone: Lab: +91-8413-235467*2044 Home: +91-40-27505833 Mobile: +91-9866147193 From sridharfirst at gmail.com Tue Sep 26 19:02:04 2006 From: sridharfirst at gmail.com (Sridhar Acharya) Date: Tue, 26 Sep 2006 22:32:04 +0530 Subject: [gmx-users] Problem reading large file in g_covar Message-ID: <45195D0C.8050403@gmail.com> Hello, I am running g_covar. But the program halts with the error message that the given xtc file was not found. In fact the xtc file which is 7.1GB was very much existing. I suppose that it is a case of large file. I compiled GROMACS3.1.4 with --enable-largefile. But still the same error occurs. How to make g_covar recognise this file? ########################################################################## :-) G R O M A C S (-: GRoups of Organic Molecules in ACtion for Science :-) VERSION 3.1.4 (-: Copyright (c) 1991-2002, University of Groningen, The Netherlands This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) /users/sridhar/bin/GROMACS314_SOLARIS/SERIAL/sparc-sun-solaris2.9/ultrasparc3/bin/g_covar (-: Option Filename Type Description ------------------------------------------------------------ -f 50NS_WT.xtc Input Generic trajectory: xtc trr trj gro g96 pdb -s ../FILES/b4md_1cyp_WT.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb -n ../FILES/pr_1cyp_WT.ndx Input, Opt! Index file -o eigenval_WT.xvg Output xvgr/xmgr file -v eigenvec_WT.trr Output Full precision trajectory: trr trj -av average_WT.pdb Output Generic structure: gro g96 pdb -l covar_WT.log Output Log file -xpm covar.xpm Output, Opt. X PixMap compatible matrix file -xpma covara.xpm Output, Opt. X PixMap compatible matrix file Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -nice int 0 Set the nicelevel -b time 12000 First frame (ps) to read from trajectory -e time 50000 Last frame (ps) to read from trajectory -dt time -1 Only use frame when t MOD dt = first time (ps) -tu enum ps Time unit: ps, fs, ns, us, ms, s, m or h -[no]fit bool yes Fit to a reference structure -[no]ref bool no Use the deviation from the conformation in the structure file instead of from the average -[no]mwa bool no Mass-weighted covariance analysis -last int -1 Last eigenvector to write away (-1 is till the last) Reading file ../FILES/b4md_1cyp_WT.tpr, VERSION 3.1.4 (single precision) Reading file ../FILES/b4md_1cyp_WT.tpr, VERSION 3.1.4 (single precision) Choose a group for the least squares fit Group 0 ( System) has 41820 elements Group 1 ( Protein) has 4858 elements Group 2 ( Protein-H) has 3775 elements Group 3 ( C-alpha) has 478 elements Group 4 ( Backbone) has 1434 elements Group 5 ( MainChain) has 1913 elements Group 6 (MainChain+Cb) has 2361 elements Group 7 ( MainChain+H) has 2363 elements Group 8 ( SideChain) has 2495 elements Group 9 ( SideChain-H) has 1862 elements Group 10 ( Prot-Masses) has 4858 elements Group 11 ( Non-Protein) has 36962 elements Group 12 ( HEME) has 47 elements Group 13 ( SOL) has 36912 elements Group 14 ( CL-) has 3 elements Group 15 ( Other) has 36962 elements Group 16 (Protein_HEME) has 4905 elements Group 17 (Protein_HEME_CL-) has 4908 elements Select a group: 3 Choose a group for the covariance analysis Group 0 ( System) has 41820 elements Group 1 ( Protein) has 4858 elements Group 2 ( Protein-H) has 3775 elements Group 3 ( C-alpha) has 478 elements Group 4 ( Backbone) has 1434 elements Group 5 ( MainChain) has 1913 elements Group 6 (MainChain+Cb) has 2361 elements Group 7 ( MainChain+H) has 2363 elements Group 8 ( SideChain) has 2495 elements Group 9 ( SideChain-H) has 1862 elements Group 10 ( Prot-Masses) has 4858 elements Group 11 ( Non-Protein) has 36962 elements Group 12 ( HEME) has 47 elements Group 13 ( SOL) has 36912 elements Group 14 ( CL-) has 3 elements Group 15 ( Other) has 36962 elements Group 16 (Protein_HEME) has 4905 elements Group 17 (Protein_HEME_CL-) has 4908 elements Select a group: 3 Note: the fit and analysis group are identical, while the fit is mass weighted and the analysis is not. Making the fit non mass weighted. Constructing covariance matrix (1434x1434)... Fatal error: File 50NS_WT.xtc not found ################################################################################# -- Sridhar Acharya, M Senior Research Fellow Lab of Computational Biology CDFD, Gandipet Campus Hyderabad. AP. INDIA http://www.cdfd.org.in email: sridhar at cdfd.org.in sridharfirst at gmail.com sridharacharya at indiatimes.com Phone: Lab: +91-8413-235467*2044 Home: +91-40-27505833 Mobile: +91-9866147193 From wjallen at vt.edu Tue Sep 26 19:30:12 2006 From: wjallen at vt.edu (wjallen at vt.edu) Date: Tue, 26 Sep 2006 13:30:12 -0400 Subject: [gmx-users] Covalent bonds between topology files Message-ID: <1159291812.451963a4be421@webmail.vt.edu> Thank you for your reply, Mark. That is what I was afraid of, that I would have to physically combine the files. My only problem there is the format of the topology file that comes from pdb2gmx is slightly different than that which comes from the PRODRG server. For example, under the [ bonds ] section: (from pdb2gmx): ... 5234 5236 2 gb_2 5237 5238 2 gb_4 ... (and from PRODRG): ... 5252 5254 1 0.140 334720.0 0.140 334720.0 CAY NBN 5254 5255 1 0.100 374468.0 0.100 374468.0 NBN HAF ... I will try to decipher this and see what comes of it. Thankfully, the renumbering of atoms was not a problem because of the reorder.pl script available in the user contributions section. Again, thank you for your reply Mark, I hope all that I said has made sense. Cheers, W. Allen From arun.target at gmail.com Tue Sep 26 20:33:39 2006 From: arun.target at gmail.com (ARUN KUMAR) Date: Wed, 27 Sep 2006 00:03:39 +0530 Subject: [gmx-users] Regarding preparation of .itp file for a new molecule Message-ID: Hai all... I am a newbie to gromacs simulation software and its file formats. I want to develop coarse grain models for surfactant systems by using atomistic simulations. I got a .pdb file for BTMAC surfactant. But to run simuations on gromacs,I need to include .itp file in source code. Can anyone of u tell me,Is it difficult to prepare a .itp file for a new molecule?? If it is so, I want to know how many days it will take to prepare....... And also Please tell suggestions to prepare a .itp file for a new molecule.... Thanks in advance -- Arun kumar.V M.E Chemical Engg -------------- next part -------------- An HTML attachment was scrubbed... URL: From tsjerkw at gmail.com Tue Sep 26 21:38:38 2006 From: tsjerkw at gmail.com (Tsjerk Wassenaar) Date: Tue, 26 Sep 2006 21:38:38 +0200 Subject: [gmx-users] Covalent bonds between topology files In-Reply-To: <1159291812.451963a4be421@webmail.vt.edu> References: <1159291812.451963a4be421@webmail.vt.edu> Message-ID: <8ff898150609261238p350c88a6q8879ed70703037e2@mail.gmail.com> Hi W. Allen, This is not necessarily a problem. The gb_* labels can be found in the ffG*bon.itp files, and are replaced by the values found in those files upon preprocessing. If they both correspond to the same force field, it's no problem to combine them with some parameters referred to by codes and others written in full. You may have to worry though, regarding the force field used for both files. This should be the same for both. Best, Tsjerk On 9/26/06, wjallen at vt.edu wrote: > > > Thank you for your reply, Mark. That is what I was afraid of, that I would have > to physically combine the files. My only problem there is the format of the > topology file that comes from pdb2gmx is slightly different than that which > comes from the PRODRG server. For example, under the [ bonds ] section: > > (from pdb2gmx): > ... > 5234 5236 2 gb_2 > 5237 5238 2 gb_4 > ... > > (and from PRODRG): > ... > 5252 5254 1 0.140 334720.0 0.140 334720.0 CAY NBN > 5254 5255 1 0.100 374468.0 0.100 374468.0 NBN HAF > ... > > I will try to decipher this and see what comes of it. Thankfully, the > renumbering of atoms was not a problem because of the reorder.pl script > available in the user contributions section. Again, thank you for your reply > Mark, I hope all that I said has made sense. > > Cheers, > W. Allen > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 From mark.abraham at anu.edu.au Wed Sep 27 02:05:21 2006 From: mark.abraham at anu.edu.au (Mark Abraham) Date: Wed, 27 Sep 2006 10:05:21 +1000 (EST) Subject: [gmx-users] Covalent bonds between topology files In-Reply-To: <1159291812.451963a4be421@webmail.vt.edu> References: <1159291812.451963a4be421@webmail.vt.edu> Message-ID: <38379.150.101.115.79.1159315521.squirrel@sqmail.anu.edu.au> > Thank you for your reply, Mark. That is what I was afraid of, that I > would have > to physically combine the files. My only problem there is the format of > the > topology file that comes from pdb2gmx is slightly different than that > which > comes from the PRODRG server. For example, under the [ bonds ] section: > > (from pdb2gmx): > ... > 5234 5236 2 gb_2 > 5237 5238 2 gb_4 > ... > > (and from PRODRG): > ... > 5252 5254 1 0.140 334720.0 0.140 334720.0 CAY NBN > 5254 5255 1 0.100 374468.0 0.100 374468.0 NBN HAF > ... That's not a problem. The .itp files will have lines like "#define gb_2 " which expands to something that resembles the latter examples, except that the bonded function number is different so the parameter lists need not match. Mark From mark.abraham at anu.edu.au Wed Sep 27 02:09:07 2006 From: mark.abraham at anu.edu.au (Mark Abraham) Date: Wed, 27 Sep 2006 10:09:07 +1000 (EST) Subject: [gmx-users] Regarding preparation of .itp file for a new molecule In-Reply-To: References: Message-ID: <42702.150.101.115.79.1159315747.squirrel@sqmail.anu.edu.au> > Hai all... > I am a newbie to gromacs simulation software and its file > formats. I want to develop coarse grain models for surfactant systems by > using atomistic simulations. I got a .pdb file for BTMAC surfactant. > But to run simuations on gromacs,I need to include .itp file in > source code. Can anyone of u tell me,Is it difficult to prepare a .itp > file > for a new molecule?? If it is so, I want to know how many days it will > take > to prepare....... And also Please tell suggestions to prepare a .itp file > for a new molecule.... It is tedious but not difficult to prepare an .itp file description of a molecule. Please read chapters 4 and 5 of the manual. Consider using the PRODRG server, and/or the pdb2gmx tool. Mark From Dallas.Warren at vcp.monash.edu.au Wed Sep 27 03:33:07 2006 From: Dallas.Warren at vcp.monash.edu.au (Dallas B. Warren) Date: Wed, 27 Sep 2006 11:33:07 +1000 Subject: [gmx-users] How can I remove water and ion molecules In-Reply-To: <20060925135526.58081.qmail@web50404.mail.yahoo.com> Message-ID: <89907EA1DCFB7548A431C13A270F9DD5023813D6@prk-exch-01.vcp.local> Or you could try using the make_ndx utility, make an index file with one of the groups containing all the molecules you want to keep, then run either editconf (if want to remove them from the .gro / .pdb files) or trajconv (if want to remove them from trajectory files). Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.warren at vcp.monash.edu.au +61 3 9903 9524 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From muta.mestri at gmail.com Wed Sep 27 05:41:55 2006 From: muta.mestri at gmail.com (Viswanadham Sridhara) Date: Tue, 26 Sep 2006 23:41:55 -0400 Subject: [gmx-users] Free energy calculations Message-ID: Hello gmx-users, I wanted to know whether there are any tutorials available on free energy calculations with Gromacs. I have done some survey, but was curious to find out any "decent" tutorials available. Thanks in advance, -Vissu. -- Viswanadham Sridhara, Research Assistant, Old Dominion University, Norfolk, Va-23529. -------------- next part -------------- An HTML attachment was scrubbed... URL: From anwar at cdfd.org.in Wed Sep 27 12:08:52 2006 From: anwar at cdfd.org.in (anwar at cdfd.org.in) Date: Wed, 27 Sep 2006 03:08:52 -0700 (PDT) Subject: [gmx-users] Re: water molecules in vacuum simulation. Message-ID: <8476439.1159322167327.JavaMail.nobody@sunserver> Hi all, I am performing in vacuum simulation of a protein containing crystallographic water molecules. I want to constrain these water molecules, but pdb2gmx program doesnot generate the pr.itp for water molecules. How do I constrain these water molecules. regards Anwar ---------------------- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 anwar.m1 at gmail.com ----------------------- ---------REPLY TO------------- Date:Wed Sep 27 00:30:36 GMT+08:00 2006 FROM: gmx-users-request at gromacs.org To: gmx-users at gromacs.org Subject: gmx-users Digest, Vol 29, Issue 81 Send gmx-users mailing list submissions to gmx-users at gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-request at gromacs.org You can reach the person managing the list at gmx-users-owner at gromacs.org When replying, please edit your Subject line so it is more specific than "Re: Contents of gmx-users digest..." Today's Topics: 1. Re: water molecules in vacuum simulation. (Steffen Wolf) 2. Re: surface tension (Serge Yefimov) 3. Re: EM problem with OPLS and TIP4P (vechism at netscape.net) 4. VAL group (Owen, Michael) 5. distance restraints: -merge (Owen, Michael) 6. Re: Which POPC Bilayer to start? (Jim Fonseca) ---------------------------------------------------------------------- Message: 1 Date: Tue, 26 Sep 2006 12:10:44 +0200 From: Steffen Wolf Subject: Re: [gmx-users] water molecules in vacuum simulation. To: Discussion list for GROMACS users Message-ID: <4518FCA4.1080305 at bph.rub.de> Content-Type: text/plain; charset=ISO-8859-1 Hi Anwar, the answer is: Yes, sure. CU Steffen > Dear users, > Is it possible to perform an invacuum simulation with few constrained water > molecules? I dont want to use the explicit solvent, but want to use the > crystallographic water molecules in protein and perform invacuum simulation. > regards > Anwar > > ---------------------- > Mohd Anwaruddin > Project Assistant > C/o DR.H.A.Nagarajaram > Lab of Computational Biology and Bioinformatics > Center for DNA Fingerprinting and Diagnostics(CDFD) > Nacharam > Hyderabad-500 076 > INDIA. > Tel: +91-8413-235467,68,69,70 ext 2019 > anwar.m1 at gmail.com > ----------------------- > > > > - > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Dipl.-Chem. Steffen Wolf Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: swolf at bph.rub.de Web: http://www.bph.rub.de ------------------------------ Message: 2 Date: Tue, 26 Sep 2006 11:01:45 +0200 From: Serge Yefimov Subject: Re: [gmx-users] surface tension To: Discussion list for GROMACS users Message-ID: <4518EC79.3030407 at rug.nl> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Pri, Surface tension of 930.002 in gromacs units = 93.0002 mN/m or (dyn/cm) serge priyanka srivastava wrote: > Dear all, > > what is the unit of surface tension in gromacs > analysis? Is it dyn/cm or N/m. As according to me it > is coming out to be in terms of N/m but it is attached > with a conversion factor of some powers of 10. > Kindly guide me. If I am getting e.g. 930.002 as the > surface tension then what are it's units? > > regards, > Pri... ------------------------------ Message: 3 Date: Tue, 26 Sep 2006 09:22:46 -0400 From: vechism at netscape.net Subject: Re: [gmx-users] EM problem with OPLS and TIP4P To: gmx-users at gromacs.org Message-ID: <8C8AF85FDD3E3A3-1784-373B at FWM-M35.sysops.aol.com> Content-Type: text/plain; charset="us-ascii" -----Original Message----- From: chris.neale at utoronto.ca To: gmx-users at gromacs.org Sent: Wed, 20 Sep 2006 10:28 PM Subject: [gmx-users] EM problem with OPLS and TIP4P Try this: unconstrained_start = no Also ensure that your .top file is correct. Also take a look at your starting positions, where is MW? Also ensure that your waters have the correct order: eg. 871SOL OW 3496 1.935 2.093 1.901 871SOL HW1 3497 1.902 2.172 1.945 871SOL HW2 3498 1.990 2.126 1.830 871SOL MW 3499 1.938 2.107 1.898 The problema was here. In my old tip4p.itp file the water sites were in reverse order. I just change the order and it works now. Thanks. Also try outputting coords for step 20,21,22,23 in the first system and see what is actually happening. _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ________________________________________________________________________ Check Out the new free AIM(R) Mail -- 2 GB of storage and industry-leading spam and email virus protection. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20060926/1a93ad45/attachment-0001.html ------------------------------ Message: 4 Date: Tue, 26 Sep 2006 10:59:08 -0500 From: "Owen, Michael" Subject: [gmx-users] VAL group To: Message-ID: <80C4D42673F70F4B9333B9F3AFFCC5081D8823 at EXBE06.blue.jays.creighton.edu> Content-Type: text/plain; charset="iso-8859-1" Hello fellow gmx users, when I convert a pdb file of a peptide that contains a valyl residue into a .gro file a separate "group" is made for the atoms in the valyl residue. This has happened when OPLSAA/l and the GROMOS96 53a6 force fields were used. The molecule appears as one in the topology file, and the atomic description of the valyl residue in the pdb file matches that of the ffoplsa.rtp file. An excert from the topology file that shows the structure contains one peptide is below. [ system ] ; Name Protein in water [ molecules ] ; Compound #mols Protein 1 SOL 6973 An excerpt from my index file that shows the VAL group, with 16 atoms that are separated from the protein is below: 28125 28126 28127 28128 28129 28130 28131 28132 28133 28134 28135 28136 28137 28138 28139 28140 28141 28142 28143 28144 28145 28146 28147 28148 28149 28150 28151 28152 28153 28154 28155 28156 28157 28158 28159 28160 28161 28162 [ VAL ] 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 [ SOL ] 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 Could something be wrong with the pdb2gmx program? Thank you in advance for any suggestions. Sincerely, Michael Owen -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20060926/d17613e0/attachment-0001.html ------------------------------ Message: 5 Date: Tue, 26 Sep 2006 11:10:15 -0500 From: "Owen, Michael" Subject: [gmx-users] distance restraints: -merge To: Message-ID: <80C4D42673F70F4B9333B9F3AFFCC5081D8824 at EXBE06.blue.jays.creighton.edu> Content-Type: text/plain; charset="iso-8859-1" Fellow gmx-users, I would like to constrain the distance of an ion to specific atoms of a protein. I recently read a message in which the use of the option -merge in the pdb2gmx program was suggested. How can I use this option to form these constraints? Thank you for your assistance, Michael Owen -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20060926/3433c22c/attachment-0001.html ------------------------------ Message: 6 Date: Tue, 26 Sep 2006 12:18:53 -0400 From: Jim Fonseca Subject: Re: [gmx-users] Which POPC Bilayer to start? To: akshay17 at olemiss.edu, Discussion list for GROMACS users Message-ID: <70FB90EC-756C-4B1E-BBCB-6AA4DD993F3F at ohiou.edu> Content-Type: text/plain; charset="us-ascii" I've had success with Tieleman's lipids. I used popc128b.pdb. Since it has the extra ns of equilibration, I figured it would cause fewer problems. However, once you start messing around with making hole in the membrane and adding a protein, you'll need to re-equilibrate again (EM & PR). Jim On Sep 20, 2006, at 5:48 PM, Akshay Patny wrote: > Hi All > > I am trying to use POPC bilayer for doing GPCR simulation. > > I have come across two options of generating a POPC bilayer >>>> > > 1. I can generate a POPC bilayer from the VMD Membrane plug-in, > wherein the > membrane is generated from the pre-built membrane square patches > and lipid > tails are (almost) fully extended. > 2. Alternatively, I can download the pre-equilibrated POPC bilayer > from Dr. > Tieleman's website, http://moose.bio.ucalgary.ca/index.php?page=People > > Since, I am new to the GPCR-membrane modeling, can you suggest me > which out > of the above two options can be a better starting point for the > simulation > of my GPCR protein? A membrane generated from VMD or a pre- > equilibrated > membrane?? Would the equilibration time for my protein be lesser in > one out > of the two? > > If option 2 is a good idea then out of popc128a.pdb and > popc128b.pdb (both > available from Prof. Tieleman's website), which will be a better > model to > start with? > > Thank you very much in advance. > Akshay > > Akshay Patny > > Graduate Research Assistant > Faser Hall 417, Department of Medicinal Chemistry > Research Institute of Pharmaceutical Sciences > University of Mississippi > University, MS 38677 > E-mail: akshay17 at olemiss.edu > Tel: 662-915-1286 (office); Web: www.olemiss.edu > > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20060926/5fd1f79e/attachment.html ------------------------------ _______________________________________________ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users End of gmx-users Digest, Vol 29, Issue 81 ***************************************** - From quantrum75 at yahoo.com Wed Sep 27 06:59:50 2006 From: quantrum75 at yahoo.com (Rama Gullapalli) Date: Tue, 26 Sep 2006 21:59:50 -0700 (PDT) Subject: [gmx-users] g_rotacf again Message-ID: <20060927045950.6418.qmail@web31410.mail.mud.yahoo.com> Hello everybody. I have question regarding g_rotacf If I wanted to compute the rotational correlation function of a linear vector which is between the "centers of masses" of two groups of atoms in an individual molecule (Instead of two atoms), how do I go about it? Can I use g_rotacf to do it ? Thanks in advance Rama --------------------------------- Talk is cheap. Use Yahoo! Messenger to make PC-to-Phone calls. Great rates starting at 1?/min. -------------- next part -------------- An HTML attachment was scrubbed... URL: From tsjerkw at gmail.com Wed Sep 27 10:37:39 2006 From: tsjerkw at gmail.com (Tsjerk Wassenaar) Date: Wed, 27 Sep 2006 10:37:39 +0200 Subject: [gmx-users] Re: water molecules in vacuum simulation. In-Reply-To: <8476439.1159322167327.JavaMail.nobody@sunserver> References: <8476439.1159322167327.JavaMail.nobody@sunserver> Message-ID: <8ff898150609270137k2c7f1b5av3897002759b51362@mail.gmail.com> Hi Anwar, The constraints are defined in spc.itp (or any of the other water models). So if you use -DPOSRES they are included automatically. Best, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 From tsjerkw at gmail.com Wed Sep 27 11:47:31 2006 From: tsjerkw at gmail.com (Tsjerk Wassenaar) Date: Wed, 27 Sep 2006 11:47:31 +0200 Subject: [gmx-users] g_rotacf again In-Reply-To: <20060927045950.6418.qmail@web31410.mail.mud.yahoo.com> References: <20060927045950.6418.qmail@web31410.mail.mud.yahoo.com> Message-ID: <8ff898150609270247n2ae5d86ax966695e332ff0940@mail.gmail.com> Hi Rama, You would be able to do it by taking one of two approaches: 1. Write the centers of masses and from this generate a multipdb file (or gro file) containing three atoms spanning two vectors perpendicular to the vector between these centers of masses. This trajectory can be used for g_rotacf (although you may need a proper run input file to go with it), according to the description given by g_rotacf -h. 2. Hack gmx_rotacf.c to calculate the rcf of the vector betwee centers of masses rather than between the cross product of two vectors between three atoms given. I think the latter option is easiest (if you can program a bit). Hope it helps, Tsjerk On 9/27/06, Rama Gullapalli wrote: > Hello everybody. > I have question regarding g_rotacf > > If I wanted to compute the rotational correlation function of a linear > vector which is between the "centers of masses" of two groups of atoms in an > individual molecule (Instead of two atoms), how do I go about it? > > Can I use g_rotacf to do it ? > Thanks in advance > Rama > > > > > > ________________________________ > Talk is cheap. Use Yahoo! Messenger to make PC-to-Phone calls. Great rates > starting at 1?/min. > > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > -- Tsjerk A. Wassenaar, Ph.D. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 From gmx3 at hotmail.com Wed Sep 27 12:14:50 2006 From: gmx3 at hotmail.com (Berk Hess) Date: Wed, 27 Sep 2006 12:14:50 +0200 Subject: [gmx-users] distance restraints: -merge In-Reply-To: <80C4D42673F70F4B9333B9F3AFFCC5081D8824@EXBE06.blue.jays.creighton.edu> Message-ID: >From: "Owen, Michael" >Reply-To: Discussion list for GROMACS users >To: >Subject: [gmx-users] distance restraints: -merge >Date: Tue, 26 Sep 2006 11:10:15 -0500 > > >Fellow gmx-users, > >I would like to constrain the distance of an ion to specific atoms of a >protein. I recently read a message in which the use of the option -merge >in the pdb2gmx program was suggested. How can I use this option to form >these constraints? The -merge option is useful for merge two molecules. I assume that in your case the ion consists of just one atom. Then it is easier to just add this one atom by hand at the end of atoms of your protein and add the distance restraint. Berk. From zarrab_m at yahoo.com Wed Sep 27 12:11:20 2006 From: zarrab_m at yahoo.com (mahbubeh zarrabi) Date: Wed, 27 Sep 2006 03:11:20 -0700 (PDT) Subject: [gmx-users] contact Message-ID: <20060927101120.60601.qmail@web51608.mail.yahoo.com> Dear freinds I want to analyz the formed contact in during the MD.How can i do with gromacs? best regard __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From Mark.Abraham at anu.edu.au Wed Sep 27 14:42:28 2006 From: Mark.Abraham at anu.edu.au (Mark Abraham) Date: Wed, 27 Sep 2006 22:42:28 +1000 Subject: [gmx-users] contact In-Reply-To: <20060927101120.60601.qmail@web51608.mail.yahoo.com> References: <20060927101120.60601.qmail@web51608.mail.yahoo.com> Message-ID: <451A71B4.8090408@anu.edu.au> mahbubeh zarrabi wrote: > Dear freinds > I want to analyz the formed contact in during the > MD.How can i do with gromacs? Read section 7.4 of the manual. Mark From sgourn at rpi.edu Wed Sep 27 15:05:17 2006 From: sgourn at rpi.edu (Nikos Sgourakis) Date: Wed, 27 Sep 2006 9:05:17 -0400 Subject: [gmx-users] g_cluster -dm Message-ID: <200609271305.k8RD5HaU010717@smtp6.server.rpi.edu> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From Mark.Abraham at anu.edu.au Wed Sep 27 16:30:19 2006 From: Mark.Abraham at anu.edu.au (Mark Abraham) Date: Thu, 28 Sep 2006 00:30:19 +1000 Subject: [gmx-users] g_cluster -dm In-Reply-To: <200609271305.k8RD5HaU010717@smtp6.server.rpi.edu> References: <200609271305.k8RD5HaU010717@smtp6.server.rpi.edu> Message-ID: <451A8AFB.7030809@anu.edu.au> Nikos Sgourakis wrote: > Hello, > > I am trying to use g_cluster. However, the result I am obtaining when > using a pre-calculated RMSD matrix with the -dm option is quite > different than the one I get when the RMSD matrix is calculated by > g_cluster from a trjectory of structures. Is this a matter of precision > in the xpm file? Have you tried comparing the output with -o with your "pre-calculated" .xpm file? Are you sure they're being generated from the same source? Mark From jianhuitian at gmail.com Wed Sep 27 17:01:49 2006 From: jianhuitian at gmail.com (Jianhui Tian) Date: Wed, 27 Sep 2006 11:01:49 -0400 Subject: [gmx-users] Fatal error: Shake block crossing node boundaries Message-ID: <1ea820a30609270801h7b67ae30vc74c0cd8f9a04b91@mail.gmail.com> Hi GMX-Users, I got an error message when using gromacs on 2 processors on the same computer. The error message is like this: _________________________________________________________________ splitting topology... Walking down the molecule graph to make shake-blocks There are 24390 charge group borders and 26054 shake borders There are 24390 total borders Division over nodes in atoms: 21234 21234 ------------------------------------------------------- Program grompp_d, VERSION 3.3 Source code file: splitter.c, line: 121 Fatal error: Shake block crossing node boundaries constraint between atoms (21226,21234) ------------------------------------------------------- ________________________________________________________________ I saw one people had similiar problems before with 8 processors, one suggestion for him was to use at most 3 or 4 processors. I tried not to use shake and the system can be ran on 2 processors well. Thanks a lot in advance. Best Regards, Justin From ecaballe at uoregon.edu Wed Sep 27 16:25:47 2006 From: ecaballe at uoregon.edu (Esther Caballero-Manrique) Date: Wed, 27 Sep 2006 07:25:47 -0700 Subject: [gmx-users] Free energy calculations In-Reply-To: References: Message-ID: <451A89EB.2090805@uoregon.edu> http://md.chem.rug.nl/education/Free-Energy_Course/index.html http://www.dillgroup.ucsf.edu/~jchodera/group/wiki/index.php/Free_Energy:_Tutorial Both very "decent". Esther Caballero-Manrique Guenza Group University of Oregon Eugene, OR (USA) Viswanadham Sridhara wrote: > Hello gmx-users, > > I wanted to know whether there are any tutorials available on free > energy calculations with Gromacs. > I have done some survey, but was curious to find out any "decent" > tutorials available. > > Thanks in advance, > -Vissu. > > -- > Viswanadham Sridhara, > Research Assistant, > Old Dominion University, > Norfolk, Va-23529. > >------------------------------------------------------------------------ > >_______________________________________________ >gmx-users mailing list gmx-users at gromacs.org >http://www.gromacs.org/mailman/listinfo/gmx-users >Please don't post (un)subscribe requests to the list. Use the >www interface or send it to gmx-users-request at gromacs.org. >Can't post? Read http://www.gromacs.org/mailing_lists/users.php > From ninoomani at yahoo.co.in Wed Sep 27 18:07:03 2006 From: ninoomani at yahoo.co.in (ninoo mani) Date: Wed, 27 Sep 2006 17:07:03 +0100 (BST) Subject: [gmx-users] g_rms, matrix and raw data In-Reply-To: <44375.150.101.115.79.1159261434.squirrel@sqmail.anu.edu.au> Message-ID: <20060927160703.98947.qmail@web8810.mail.in.yahoo.com> Dear Mark I read the manual but I could not find any option to get the original values of the matrix. I will be highly appreciative if you can help. thanks Ninoo Mani --- Mark Abraham wrote: > > Dear all > > > > I run g_rms with -m option that produces a matrix > in > > .xpm format. Is it possible somehow to obtain raw > data > > i.e. the real numerical values of the elements of > the > > matrix? > > man g_rms > > Mark > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the > list. Use the > www interface or send it to > gmx-users-request at gromacs.org. > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > __________________________________________________________ Yahoo! India Answers: Share what you know. Learn something new http://in.answers.yahoo.com/ From aroberts99163 at yahoo.com Wed Sep 27 18:40:38 2006 From: aroberts99163 at yahoo.com (Arthur Roberts) Date: Wed, 27 Sep 2006 09:40:38 -0700 (PDT) Subject: [gmx-users] gromacs 3.3.1 with fftw 3.12 and the current version of AIX 5.2 Message-ID: <20060927164038.16656.qmail@web38809.mail.mud.yahoo.com> Hi, all, Has anyone out there successfully compiled gromacs 3.3.1 with fftw 3.12 and the current version of AIX 5.2 on a Bluegene server? I am not sure how the environment variables should be set. Your input would be much appreciated. Best wishes, Art From tsjerkw at gmail.com Wed Sep 27 20:20:21 2006 From: tsjerkw at gmail.com (Tsjerk Wassenaar) Date: Wed, 27 Sep 2006 20:20:21 +0200 Subject: [gmx-users] g_rms, matrix and raw data In-Reply-To: <20060927160703.98947.qmail@web8810.mail.in.yahoo.com> References: <44375.150.101.115.79.1159261434.squirrel@sqmail.anu.edu.au> <20060927160703.98947.qmail@web8810.mail.in.yahoo.com> Message-ID: <8ff898150609271120g65031545wa90b0efb418c924e@mail.gmail.com> Hi Ninoo, You can hack the code of gmx_rms.c in [GMXSRCDIR]/src/tools/ to output the matrix generated into a human readable format. It is also possible to write a raw binary file which can easily be processed using a scripting language such as python (use g_rms -bin). Best, Tsjerk On 9/27/06, ninoo mani wrote: > Dear Mark > I read the manual but I could not find any option to > get the original values of the matrix. I will be > highly appreciative if you can help. > thanks > Ninoo Mani > > > --- Mark Abraham wrote: > > > > Dear all > > > > > > I run g_rms with -m option that produces a matrix > > in > > > .xpm format. Is it possible somehow to obtain raw > > data > > > i.e. the real numerical values of the elements of > > the > > > matrix? > > > > man g_rms > > > > Mark > > > > _______________________________________________ > > gmx-users mailing list gmx-users at gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the > > list. Use the > > www interface or send it to > > gmx-users-request at gromacs.org. > > Can't post? Read > > http://www.gromacs.org/mailing_lists/users.php > > > > > > __________________________________________________________ > Yahoo! India Answers: Share what you know. Learn something new > http://in.answers.yahoo.com/ > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 From asaraujo at if.sc.usp.br Wed Sep 27 18:30:56 2006 From: asaraujo at if.sc.usp.br (Alexandre Suman de Araujo) Date: Wed, 27 Sep 2006 16:30:56 +0000 Subject: [gmx-users] Problems in bonded parameters for nitrate with OPLS in GROMACS Message-ID: <451AA740.6070606@if.sc.usp.br> Hi GMXers I'm trying to use in my simulations the nitrate ion defined in OPLS (ffoplsaa.atp) force field as atom-types opls_787 and opls_788, but when I look at OPLS bonded parameters in ffoplsaabon.itp I can't find bonds, angles or dihedral parameters with it's bond_type (N and O as defined in ffoplsaanb.itp). Are these bond_types correct? If yes, where are the bond parameters for them? Does anybody know the paper where these parameter were published? Thank's -- Alexandre Suman de Araujo asaraujo at if.sc.usp.br UIN: 6194055 IFSC - USP - S?o Carlos - Brasil From paloureiro at biof.ufrj.br Wed Sep 27 21:54:48 2006 From: paloureiro at biof.ufrj.br (Pedro Alexandre Lapido Loureiro) Date: Wed, 27 Sep 2006 16:54:48 -0300 Subject: [gmx-users] density map Message-ID: <20060927165448.d8qahjiyypcsgso4@webmail.biof.ufrj.br> Hi, how can I get the number density values from g_densmap? I would like to "play" with these values, such as finding the points of greatest density, for instance. Regards. Pedro. ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From carlosjn at ce.fis.unam.mx Thu Sep 28 03:50:34 2006 From: carlosjn at ce.fis.unam.mx (=?ISO-8859-1?Q?Carlos_Javier_Nu=F1ez_Aguero?=) Date: Wed, 27 Sep 2006 20:50:34 -0500 Subject: [gmx-users] Free energy calculations In-Reply-To: References: Message-ID: <451B2A6A.1050801@ce.fis.unam.mx> Hi, the review by David Pearlman can be very useful in relation to FEP-type calculations o Free Energy Calculations: Methods for Estimating Ligand Binding Affinities Chapter 2 In: Free energy calculations in rational drug design M. Rami Reddy & Mark D. Erion Eds. Best regards, Javier N. Viswanadham Sridhara wrote: > Hello gmx-users, > > I wanted to know whether there are any tutorials available on free > energy calculations with Gromacs. > I have done some survey, but was curious to find out any "decent" > tutorials available. > > Thanks in advance, > -Vissu. > > -- > Viswanadham Sridhara, > Research Assistant, > Old Dominion University, > Norfolk, Va-23529. -- No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.1.407 / Virus Database: 268.12.9/458 - Release Date: 9/27/2006 From anwar at cdfd.org.in Thu Sep 28 16:59:52 2006 From: anwar at cdfd.org.in (anwar at cdfd.org.in) Date: Thu, 28 Sep 2006 07:59:52 -0700 (PDT) Subject: [gmx-users] Re: water molecules in vacuum simulation Message-ID: <28942473.1159426026041.JavaMail.nobody@sunserver> Hi all, I am facing a problem in constraining the crystallographic water molecules during invacuo simulation. Even after including the oxygen atom numbers in the .top file for position restrain (given below), the dynamics is going the same way as it was without positoion restrain. Please Help me out of this. #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 12448 1 1000 1000 1000 12451 1 1000 1000 1000 12454 1 1000 1000 1000 12457 1 1000 1000 1000 12460 1 1000 1000 1000 12463 1 1000 1000 1000 12466 1 1000 1000 1000 12469 1 1000 1000 1000 12472 1 1000 1000 1000 12475 1 1000 1000 1000 12478 1 1000 1000 1000 12481 1 1000 1000 1000 12484 1 1000 1000 1000 12487 1 1000 1000 1000 12490 1 1000 1000 1000 12493 1 1000 1000 1000 12496 1 1000 1000 1000 12499 1 1000 1000 1000 12502 1 1000 1000 1000 12405 1 1000 1000 1000 #endif regards Anwar ---------------------- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 anwar.m1 at gmail.com ----------------------- - From zzhwise1 at 163.com Thu Sep 28 14:38:56 2006 From: zzhwise1 at 163.com (zzhwise1) Date: Thu, 28 Sep 2006 20:38:56 +0800 (CST) Subject: [gmx-users] energy minimization end too early! Message-ID: <451BC260.00008B.27975@bj163app88.163.com> hi everyone today ,I do minimization with my system,my system with two face to face monolayers composed of ch3(ch2)13cooh, when i set the molecular as CHO group,it pass smoothly,because i want to pull the upper layer ,so i set the upper layer group DHO that has the same parameters with CHO itp , but the mdrun only reached 22th step and finished normally,which is too few to 5000 steps! i want why ! -------------- next part -------------- An HTML attachment was scrubbed... URL: From pedros at ufp.pt Thu Sep 28 15:01:31 2006 From: pedros at ufp.pt (pedros at ufp.pt) Date: Thu, 28 Sep 2006 14:01:31 +0100 Subject: [gmx-users] QMMM interface Message-ID: <20060928140131.i1nk3bcu6g408c4c@webmail.ufp.pt> Dear Gromacs users, I have been using Pcgamess for QM calculations, which is a very fast (and free) program, and has some QMMM capabilities(but a size limit of about 1000 atoms ). I just found out that Gromacs now has QMMM capabilities with CPMD, Gaussian and Gamess(UK). Does any one know whether a Gromacs-PcGamess QMMM interface is planned? It would be great for those of us with small research budgets, and who cannot afford the comercial QM codes. Pedro ---------------------------------------------------------------- Enviado por https://webmail.ufp.pt From tsjerkw at gmail.com Thu Sep 28 15:08:47 2006 From: tsjerkw at gmail.com (Tsjerk Wassenaar) Date: Thu, 28 Sep 2006 15:08:47 +0200 Subject: [gmx-users] energy minimization end too early! In-Reply-To: <451BC260.00008B.27975@bj163app88.163.com> References: <451BC260.00008B.27975@bj163app88.163.com> Message-ID: <8ff898150609280608w4305a048vdcc5f89ca84266c@mail.gmail.com> Hi Zzhwise1, Energy minimization does not need to run all steps. You define a maximum number, but maybe the minimum is already reached before that. On the other hand, the energy may have gone to infinity, which usually puts an end to minimization. Check the energies you get during/after minimization. Check for overlaps, bad starting structures, bad box, etc. Tsjerk On 9/28/06, zzhwise1 wrote: > hi everyone > today ,I do minimization with my system,my system with two face to face > monolayers composed of ch3(ch2)13cooh, > when i set the molecular as CHO group,it pass smoothly,because i want to > pull the upper layer ,so i set the upper layer group DHO that has the same > parameters with CHO itp , but the mdrun only reached 22th step and finished > normally,which is too few to 5000 steps! > i want why ! > > > > > > > ? ? ? ??? ? ? ? > ? ? ? ? ? ? ? ??? ? ? ? ? ? ? ? ? ? ? > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > -- Tsjerk A. Wassenaar, Ph.D. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 From dmobley at gmail.com Thu Sep 28 17:42:46 2006 From: dmobley at gmail.com (David Mobley) Date: Thu, 28 Sep 2006 08:42:46 -0700 Subject: [gmx-users] Re: water molecules in vacuum simulation In-Reply-To: <28942473.1159426026041.JavaMail.nobody@sunserver> References: <28942473.1159426026041.JavaMail.nobody@sunserver> Message-ID: This may be naive, but have you defined POSRES_WATER, i.e. in your top or mdp file? If not, the position restraints will be unused. On 9/28/06, anwar at cdfd.org.in wrote: > Hi all, > I am facing a problem in constraining the crystallographic water molecules > during invacuo simulation. Even after including the oxygen atom numbers > in the .top file for position restrain (given below), the dynamics is going > the same way as it was without positoion restrain. Please Help me out of > this. > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcx fcy fcz > 12448 1 1000 1000 1000 > 12451 1 1000 1000 1000 > 12454 1 1000 1000 1000 > 12457 1 1000 1000 1000 > 12460 1 1000 1000 1000 > 12463 1 1000 1000 1000 > 12466 1 1000 1000 1000 > 12469 1 1000 1000 1000 > 12472 1 1000 1000 1000 > 12475 1 1000 1000 1000 > 12478 1 1000 1000 1000 > 12481 1 1000 1000 1000 > 12484 1 1000 1000 1000 > 12487 1 1000 1000 1000 > 12490 1 1000 1000 1000 > 12493 1 1000 1000 1000 > 12496 1 1000 1000 1000 > 12499 1 1000 1000 1000 > 12502 1 1000 1000 1000 > 12405 1 1000 1000 1000 > #endif > > regards > Anwar > ---------------------- > Mohd Anwaruddin > Project Assistant > C/o DR.H.A.Nagarajaram > Lab of Computational Biology and Bioinformatics > Center for DNA Fingerprinting and Diagnostics(CDFD) > Nacharam > Hyderabad-500 076 > INDIA. > Tel: +91-8413-235467,68,69,70 ext 2019 > anwar.m1 at gmail.com > ----------------------- > > > > - > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > From acorrea at unisa.it Thu Sep 28 18:05:53 2006 From: acorrea at unisa.it (andrea correa) Date: Thu, 28 Sep 2006 18:05:53 +0200 Subject: [gmx-users] Job Vacancy -MolNaC University of Salerno Message-ID: <200609281805.53193.acorrea@unisa.it> Applications are invited for a postdoctoral position in computational chemistry in the group of Luigi Cavallo in the Department of Chemistry at the University of Salerno, Italy. The initial appointment is for one year, with the possibility to renew for a second year on the condition that research funds are available. Candidates should have a Ph.D. in Chemistry, Physics, or related fields. A strong background in computational chemistry and programming skills are essential. The main theme of our research is to develop and apply state-of-the-art computational tools (electronic structure calculations, mainly) to achieve an understanding of reaction mechanisms and of intermolecular interactions. The systems of primary interest are organometallic complexes for homogeneous catalysis. For more information see http://www.chem.unisa.it/groups/molnac/. Interested candidates should send a letter of intent and a C.V. (by e-mail to lcavallo-at-unisa.it), and arrange for two letters of recommendation. From muta.mestri at gmail.com Thu Sep 28 19:48:50 2006 From: muta.mestri at gmail.com (Viswanadham Sridhara) Date: Thu, 28 Sep 2006 13:48:50 -0400 Subject: [gmx-users] cardiolipin / Cytochrome C Message-ID: Hello gmx users, Were there any previous molecular dynamics simulations done on cardiolipin / Cytochrome C binding? Any "pdb" files available for either Cardiolipin or cytochrome C,. any literature available / any tutorials. Thanks in advance, -Vissu. -- Viswanadham Sridhara, Research Assistant, Old Dominion University, Norfolk, Va-23529. -------------- next part -------------- An HTML attachment was scrubbed... URL: From scott.t.milner at exxonmobil.com Thu Sep 28 19:38:56 2006 From: scott.t.milner at exxonmobil.com (scott.t.milner at exxonmobil.com) Date: Thu, 28 Sep 2006 13:38:56 -0400 Subject: [gmx-users] defining new residues? Message-ID: Hello -- I am interested in using gromacs to simulate polymers. Apparently the .rtp files within gromacs are defined for protein residues, not typical monomers being used in polymers. I don't know anything about proteins, but I would think that there is a strong analogy between proteins and polymers, in that linear polymers are composed of a succession of monomers (often, just the same monomer repeated), joined by single covalent bonds. Typical monomers I would be interested in are methylene (-CH2-), propylene (-CH(CH3)CH2-), styrene (-CH(C6H5)CH2-), and so forth. It would be very convenient if I could add these structures as new "residues" to the definitions of some of the force fields (e.g., OPLSAA and GMX), so that I could use pdb2gmx to generate topology files for a simulation, without having to generate the topology files by hand. Is there some documentation that describes the structure of the various files associated with a force field, and what information would then be required for defining new residues? Thanks for any help you can provide -- Scott Milner ExxonMobil Research and Engineering 1545 Route 22 East Annandale, NJ 08801 (908) 730-2309 phone (262) 313-2583 fax From dong at pampas.chem.purdue.edu Thu Sep 28 21:02:05 2006 From: dong at pampas.chem.purdue.edu (Dongsheng Zhang) Date: Thu, 28 Sep 2006 15:02:05 -0400 Subject: [gmx-users] defining new residues? In-Reply-To: References: Message-ID: <1159470125.12441.20.camel@pampas.chem.purdue.edu> It is possible to generate new "residues". First of all, you need to make a decision which force field you will use for your new residues. For example, you will choose opls. then you add one building block into ffoplsaa.rtp. As you read ffoplsaa.rtp, you can see that you need to specify atoms' name, type, and the partial charge, you also need to define bonds and the dihedral angle between atoms. When you build it, you need to refer ffoplsaanb.itp ffoplsaabon.itp and ffoplsaa.atp. You might modify aminoacids.dat, ffoplsaa-n.tdb' ffoplsaa-c.tdb as well. You can read the manual to get more information. On Thu, 2006-09-28 at 13:38 -0400, scott.t.milner at exxonmobil.com wrote: > Hello -- I am interested in using gromacs to simulate polymers. Apparently > the .rtp files within gromacs are defined for protein residues, not typical > monomers being used in polymers. I don't know anything about proteins, but > I would think that there is a strong analogy between proteins and polymers, > in that linear polymers are composed of a succession of monomers (often, > just the same monomer repeated), joined by single covalent bonds. Typical > monomers I would be interested in are methylene (-CH2-), propylene > (-CH(CH3)CH2-), styrene (-CH(C6H5)CH2-), and so forth. It would be very > convenient if I could add these structures as new "residues" to the > definitions of some of the force fields (e.g., OPLSAA and GMX), so that I > could use pdb2gmx to generate topology files for a simulation, without > having to generate the topology files by hand. Is there some documentation > that describes the structure of the various files associated with a force > field, and what information would then be required for defining new > residues? > > Thanks for any help you can provide -- > > Scott Milner > ExxonMobil Research and Engineering > 1545 Route 22 East > Annandale, NJ 08801 > (908) 730-2309 phone > (262) 313-2583 fax > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php From spoel at xray.bmc.uu.se Thu Sep 28 21:07:36 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Thu, 28 Sep 2006 21:07:36 +0200 Subject: [gmx-users] defining new residues? In-Reply-To: <1159470125.12441.20.camel@pampas.chem.purdue.edu> References: <1159470125.12441.20.camel@pampas.chem.purdue.edu> Message-ID: <451C1D78.8090703@xray.bmc.uu.se> Dongsheng Zhang wrote: > It is possible to generate new "residues". First of all, you need to > make a decision which force field you will use for your new residues. > For example, you will choose opls. then you add one building block into > ffoplsaa.rtp. As you read ffoplsaa.rtp, you can see that you need to > specify atoms' name, type, and the partial charge, you also need to > define bonds and the dihedral angle between atoms. When you build it, > you need to refer ffoplsaanb.itp ffoplsaabon.itp and ffoplsaa.atp. You > might modify aminoacids.dat, ffoplsaa-n.tdb' ffoplsaa-c.tdb as well. > > > You can read the manual to get more information. > > > On Thu, 2006-09-28 at 13:38 -0400, scott.t.milner at exxonmobil.com wrote: >> Hello -- I am interested in using gromacs to simulate polymers. Apparently >> the .rtp files within gromacs are defined for protein residues, not typical >> monomers being used in polymers. I don't know anything about proteins, but >> I would think that there is a strong analogy between proteins and polymers, >> in that linear polymers are composed of a succession of monomers (often, >> just the same monomer repeated), joined by single covalent bonds. Typical >> monomers I would be interested in are methylene (-CH2-), propylene >> (-CH(CH3)CH2-), styrene (-CH(C6H5)CH2-), and so forth. It would be very >> convenient if I could add these structures as new "residues" to the >> definitions of some of the force fields (e.g., OPLSAA and GMX), so that I >> could use pdb2gmx to generate topology files for a simulation, without >> having to generate the topology files by hand. Is there some documentation >> that describes the structure of the various files associated with a force >> field, and what information would then be required for defining new >> residues? >> >> Thanks for any help you can provide -- >> >> Scott Milner >> ExxonMobil Research and Engineering >> 1545 Route 22 East >> Annandale, NJ 08801 >> (908) 730-2309 phone >> (262) 313-2583 fax >> >> _______________________________________________ >> gmx-users mailing list gmx-users at gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-request at gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php an alternative that's in the works is the x2top program, which is simpler, since it is atom based, but you need just one configuration file. if you want to see a sample send me a coordinate file off-list. you will need at least the 3.3.1 CVS version for this though. -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From rkasat at ecn.purdue.edu Thu Sep 28 20:50:41 2006 From: rkasat at ecn.purdue.edu (Rahul B Kasat) Date: Thu, 28 Sep 2006 14:50:41 -0400 (EDT) Subject: [gmx-users] defining new residues? In-Reply-To: References: Message-ID: Hi Scott You can use PRODRG (available online) for generating topologies. Then you dont have to worry about playing with pdb2gmx. Cheers, - Rahul On Thu, 28 Sep 2006 scott.t.milner at exxonmobil.com wrote: > Hello -- I am interested in using gromacs to simulate polymers. Apparently > the .rtp files within gromacs are defined for protein residues, not typical > monomers being used in polymers. I don't know anything about proteins, but > I would think that there is a strong analogy between proteins and polymers, > in that linear polymers are composed of a succession of monomers (often, > just the same monomer repeated), joined by single covalent bonds. Typical > monomers I would be interested in are methylene (-CH2-), propylene > (-CH(CH3)CH2-), styrene (-CH(C6H5)CH2-), and so forth. It would be very > convenient if I could add these structures as new "residues" to the > definitions of some of the force fields (e.g., OPLSAA and GMX), so that I > could use pdb2gmx to generate topology files for a simulation, without > having to generate the topology files by hand. Is there some documentation > that describes the structure of the various files associated with a force > field, and what information would then be required for defining new > residues? > > Thanks for any help you can provide -- > > Scott Milner > ExxonMobil Research and Engineering > 1545 Route 22 East > Annandale, NJ 08801 > (908) 730-2309 phone > (262) 313-2583 fax > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > From joyoung at uwo.ca Thu Sep 28 21:40:39 2006 From: joyoung at uwo.ca (Jason O'Young) Date: Thu, 28 Sep 2006 15:40:39 -0400 Subject: [gmx-users] Re: gmx-users Digest, Vol 29, Issue 86 In-Reply-To: <20060928190238.CCA73240B2@xray.bmc.uu.se> References: <20060928190238.CCA73240B2@xray.bmc.uu.se> Message-ID: <0DF1B32E-2348-434A-B0CB-B51C165A6EE1@uwo.ca> Yes that is fine. I don't want to go later than 5 though. Jason On 28-Sep-06, at 3:02 PM, gmx-users-request at gromacs.org wrote: > Send gmx-users mailing list submissions to > gmx-users at gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-request at gromacs.org > > You can reach the person managing the list at > gmx-users-owner at gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. energy minimization end too early! (zzhwise1) > 2. QMMM interface (pedros at ufp.pt) > 3. Re: energy minimization end too early! (Tsjerk Wassenaar) > 4. Re: Re: water molecules in vacuum simulation (David Mobley) > 5. Job Vacancy -MolNaC University of Salerno (andrea correa) > 6. cardiolipin / Cytochrome C (Viswanadham Sridhara) > 7. defining new residues? (scott.t.milner at exxonmobil.com) > 8. Re: defining new residues? (Dongsheng Zhang) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 28 Sep 2006 20:38:56 +0800 (CST) > From: "zzhwise1" > Subject: [gmx-users] energy minimization end too early! > To: "gmx-users" > Message-ID: <451BC260.00008B.27975 at bj163app88.163.com> > Content-Type: text/plain; charset="gb2312" > > hi everyone > today ,I do minimization with my system,my system with two face > to face monolayers composed of ch3(ch2)13cooh, > when i set the molecular as CHO group,it pass smoothly,because i > want to pull the upper layer ,so i set the upper layer group DHO > that has the same parameters with CHO itp , but the mdrun only > reached 22th step and finished normally,which is too few to 5000 > steps! > i want why ! > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.gromacs.org/pipermail/gmx-users/attachments/ > 20060928/0127a11b/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Thu, 28 Sep 2006 14:01:31 +0100 > From: pedros at ufp.pt > Subject: [gmx-users] QMMM interface > To: gmx-users at gromacs.org > Message-ID: <20060928140131.i1nk3bcu6g408c4c at webmail.ufp.pt> > Content-Type: text/plain; charset=ISO-8859-1; format="flowed" > > > Dear Gromacs users, > > I have been using Pcgamess for QM calculations, which is a very fast > (and free) program, and has some QMMM capabilities(but a size limit of > about 1000 atoms ). I just found out that Gromacs now has QMMM > capabilities with CPMD, Gaussian and Gamess(UK). Does any one know > whether a Gromacs-PcGamess QMMM interface is planned? It would be > great > for those of us with small research budgets, and who cannot afford the > comercial QM codes. > > Pedro > > ---------------------------------------------------------------- > Enviado por https://webmail.ufp.pt > > > > > ------------------------------ > > Message: 3 > Date: Thu, 28 Sep 2006 15:08:47 +0200 > From: "Tsjerk Wassenaar" > Subject: Re: [gmx-users] energy minimization end too early! > To: "Discussion list for GROMACS users" > Message-ID: > <8ff898150609280608w4305a048vdcc5f89ca84266c at mail.gmail.com> > Content-Type: text/plain; charset=GB2312; format=flowed > > Hi Zzhwise1, > > Energy minimization does not need to run all steps. You define a > maximum number, but maybe the minimum is already reached before that. > On the other hand, the energy may have gone to infinity, which usually > puts an end to minimization. Check the energies you get during/after > minimization. Check for overlaps, bad starting structures, bad box, > etc. > > Tsjerk > > On 9/28/06, zzhwise1 wrote: >> hi everyone >> today ,I do minimization with my system,my system with two >> face to face >> monolayers composed of ch3(ch2)13cooh, >> when i set the molecular as CHO group,it pass smoothly,because i >> want to >> pull the upper layer ,so i set the upper layer group DHO that has >> the same >> parameters with CHO itp , but the mdrun only reached 22th step and >> finished >> normally,which is too few to 5000 steps! >> i want why ! >> >> >> >> >> >> >> ?? ?? ?? ?????? ?? ?? ?? >> ?? ?? ?? ?? ?? ?? ?? ?????? ?? ?? ?? ?? ?? ?? ? ?? ?? ?? >> _______________________________________________ >> gmx-users mailing list gmx-users at gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-request at gromacs.org. >> Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php >> >> > > > -- > Tsjerk A. Wassenaar, Ph.D. > Groningen Biomolecular Sciences and Biotechnology Institute (GBB) > Dept. of Biophysical Chemistry > University of Groningen > Nijenborgh 4 > 9747AG Groningen, The Netherlands > +31 50 363 4336 > > ------------------------------ > > Message: 4 > Date: Thu, 28 Sep 2006 08:42:46 -0700 > From: "David Mobley" > Subject: Re: [gmx-users] Re: water molecules in vacuum simulation > To: "Discussion list for GROMACS users" > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > This may be naive, but have you defined POSRES_WATER, i.e. in your top > or mdp file? If not, the position restraints will be unused. > > > > On 9/28/06, anwar at cdfd.org.in wrote: >> Hi all, >> I am facing a problem in constraining the crystallographic water >> molecules >> during invacuo simulation. Even after including the oxygen atom >> numbers >> in the .top file for position restrain (given below), the dynamics >> is going >> the same way as it was without positoion restrain. Please Help me >> out of >> this. >> #ifdef POSRES_WATER >> ; Position restraint for each water oxygen >> [ position_restraints ] >> ; i funct fcx fcy fcz >> 12448 1 1000 1000 1000 >> 12451 1 1000 1000 1000 >> 12454 1 1000 1000 1000 >> 12457 1 1000 1000 1000 >> 12460 1 1000 1000 1000 >> 12463 1 1000 1000 1000 >> 12466 1 1000 1000 1000 >> 12469 1 1000 1000 1000 >> 12472 1 1000 1000 1000 >> 12475 1 1000 1000 1000 >> 12478 1 1000 1000 1000 >> 12481 1 1000 1000 1000 >> 12484 1 1000 1000 1000 >> 12487 1 1000 1000 1000 >> 12490 1 1000 1000 1000 >> 12493 1 1000 1000 1000 >> 12496 1 1000 1000 1000 >> 12499 1 1000 1000 1000 >> 12502 1 1000 1000 1000 >> 12405 1 1000 1000 1000 >> #endif >> >> regards >> Anwar >> ---------------------- >> Mohd Anwaruddin >> Project Assistant >> C/o DR.H.A.Nagarajaram >> Lab of Computational Biology and Bioinformatics >> Center for DNA Fingerprinting and Diagnostics(CDFD) >> Nacharam >> Hyderabad-500 076 >> INDIA. >> Tel: +91-8413-235467,68,69,70 ext 2019 >> anwar.m1 at gmail.com >> ----------------------- >> >> >> >> - >> >> _______________________________________________ >> gmx-users mailing list gmx-users at gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-request at gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > ------------------------------ > > Message: 5 > Date: Thu, 28 Sep 2006 18:05:53 +0200 > From: andrea correa > Subject: [gmx-users] Job Vacancy -MolNaC University of Salerno > To: "Discussion list for GROMACS users" > Cc: lcavallo at unisa.it > Message-ID: <200609281805.53193.acorrea at unisa.it> > Content-Type: text/plain; charset="us-ascii" > > > Applications are invited for a postdoctoral position in computational > chemistry in the group of Luigi Cavallo in the Department of Chemistry > at the University of Salerno, Italy. The initial appointment is for > one year, with the possibility to renew for a second year on the > condition that research funds are available. > > > Candidates should have a Ph.D. in Chemistry, Physics, or related > fields. A strong background in computational chemistry and programming > skills are essential. The main theme of our research is to develop and > apply state-of-the-art computational tools (electronic structure > calculations, mainly) to achieve an understanding of reaction > mechanisms and of intermolecular interactions. The systems of primary > interest are organometallic complexes for homogeneous catalysis. For > more information see http://www.chem.unisa.it/groups/molnac/. > > Interested candidates should send a letter of intent and a C.V. (by > e-mail to lcavallo-at-unisa.it), and arrange for two letters of > recommendation. > > > > ------------------------------ > > Message: 6 > Date: Thu, 28 Sep 2006 13:48:50 -0400 > From: "Viswanadham Sridhara" > Subject: [gmx-users] cardiolipin / Cytochrome C > To: "GROMACS list" > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hello gmx users, > > Were there any previous molecular dynamics simulations done on > cardiolipin / > Cytochrome C binding? > Any "pdb" files available for either Cardiolipin or cytochrome C,. any > literature available / any tutorials. > > Thanks in advance, > -Vissu. > > -- > Viswanadham Sridhara, > Research Assistant, > Old Dominion University, > Norfolk, Va-23529. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.gromacs.org/pipermail/gmx-users/attachments/ > 20060928/eaeced0d/attachment-0001.html > > ------------------------------ > > Message: 7 > Date: Thu, 28 Sep 2006 13:38:56 -0400 > From: scott.t.milner at exxonmobil.com > Subject: [gmx-users] defining new residues? > To: gmx-users at gromacs.org > Message-ID: > ON852571F7.005F04FE-852571F7.0060F2E0 at exxonmobil.com> > > Content-Type: text/plain; charset=US-ASCII > > Hello -- I am interested in using gromacs to simulate polymers. > Apparently > the .rtp files within gromacs are defined for protein residues, not > typical > monomers being used in polymers. I don't know anything about > proteins, but > I would think that there is a strong analogy between proteins and > polymers, > in that linear polymers are composed of a succession of monomers > (often, > just the same monomer repeated), joined by single covalent bonds. > Typical > monomers I would be interested in are methylene (-CH2-), propylene > (-CH(CH3)CH2-), styrene (-CH(C6H5)CH2-), and so forth. It would be > very > convenient if I could add these structures as new "residues" to the > definitions of some of the force fields (e.g., OPLSAA and GMX), so > that I > could use pdb2gmx to generate topology files for a simulation, without > having to generate the topology files by hand. Is there some > documentation > that describes the structure of the various files associated with a > force > field, and what information would then be required for defining new > residues? > > Thanks for any help you can provide -- > > Scott Milner > ExxonMobil Research and Engineering > 1545 Route 22 East > Annandale, NJ 08801 > (908) 730-2309 phone > (262) 313-2583 fax > > > > ------------------------------ > > Message: 8 > Date: Thu, 28 Sep 2006 15:02:05 -0400 > From: Dongsheng Zhang > Subject: Re: [gmx-users] defining new residues? > To: Discussion list for GROMACS users > Message-ID: <1159470125.12441.20.camel at pampas.chem.purdue.edu> > Content-Type: text/plain > > It is possible to generate new "residues". First of all, you need to > make a decision which force field you will use for your new residues. > For example, you will choose opls. then you add one building block > into > ffoplsaa.rtp. As you read ffoplsaa.rtp, you can see that you need to > specify atoms' name, type, and the partial charge, you also need to > define bonds and the dihedral angle between atoms. When you build it, > you need to refer ffoplsaanb.itp ffoplsaabon.itp and ffoplsaa.atp. You > might modify aminoacids.dat, ffoplsaa-n.tdb' ffoplsaa-c.tdb as well. > > > You can read the manual to get more information. > > > On Thu, 2006-09-28 at 13:38 -0400, scott.t.milner at exxonmobil.com > wrote: >> Hello -- I am interested in using gromacs to simulate polymers. >> Apparently >> the .rtp files within gromacs are defined for protein residues, >> not typical >> monomers being used in polymers. I don't know anything about >> proteins, but >> I would think that there is a strong analogy between proteins and >> polymers, >> in that linear polymers are composed of a succession of monomers >> (often, >> just the same monomer repeated), joined by single covalent bonds. >> Typical >> monomers I would be interested in are methylene (-CH2-), propylene >> (-CH(CH3)CH2-), styrene (-CH(C6H5)CH2-), and so forth. It would >> be very >> convenient if I could add these structures as new "residues" to the >> definitions of some of the force fields (e.g., OPLSAA and GMX), so >> that I >> could use pdb2gmx to generate topology files for a simulation, >> without >> having to generate the topology files by hand. Is there some >> documentation >> that describes the structure of the various files associated with >> a force >> field, and what information would then be required for defining new >> residues? >> >> Thanks for any help you can provide -- >> >> Scott Milner >> ExxonMobil Research and Engineering >> 1545 Route 22 East >> Annandale, NJ 08801 >> (908) 730-2309 phone >> (262) 313-2583 fax >> >> _______________________________________________ >> gmx-users mailing list gmx-users at gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-request at gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > > > End of gmx-users Digest, Vol 29, Issue 86 > ***************************************** From Mark.Abraham at anu.edu.au Thu Sep 28 23:50:01 2006 From: Mark.Abraham at anu.edu.au (Mark Abraham) Date: Fri, 29 Sep 2006 07:50:01 +1000 Subject: [gmx-users] defining new residues? In-Reply-To: References: Message-ID: <451C4389.9020804@anu.edu.au> scott.t.milner at exxonmobil.com wrote: > Hello -- I am interested in using gromacs to simulate polymers. Apparently > the .rtp files within gromacs are defined for protein residues, not typical > monomers being used in polymers. I don't know anything about proteins, but > I would think that there is a strong analogy between proteins and polymers, > in that linear polymers are composed of a succession of monomers (often, > just the same monomer repeated), joined by single covalent bonds. Typical > monomers I would be interested in are methylene (-CH2-), propylene > (-CH(CH3)CH2-), styrene (-CH(C6H5)CH2-), and so forth. It would be very > convenient if I could add these structures as new "residues" to the > definitions of some of the force fields (e.g., OPLSAA and GMX), so that I This would be possible, however it would be unwise to extrapolate that a force field for peptide simulations is suitable for lipid-polymer simulations without serious evidence, such as previous studies, or the force field having been developed with this use in mind. Look in the polymer literature and see what force fields are used there. Simplest will be to use the software and the force fields described there, rather than choose GROMACS and have to work something in to fit. There are polymer force fields that work with GROMACS, I just don't know what they are... > could use pdb2gmx to generate topology files for a simulation, without > having to generate the topology files by hand. Is there some documentation > that describes the structure of the various files associated with a force > field, and what information would then be required for defining new > residues? Yep. Chapters 4 and 5 of the manual. They're pretty good, but not perfect. I'd recommend playing around doing some simulations to see how the pieces fit together before tinkering seriously with force fields. Mark From Mark.Abraham at anu.edu.au Thu Sep 28 23:52:28 2006 From: Mark.Abraham at anu.edu.au (Mark Abraham) Date: Fri, 29 Sep 2006 07:52:28 +1000 Subject: [gmx-users] cardiolipin / Cytochrome C In-Reply-To: References: Message-ID: <451C441C.1040808@anu.edu.au> Viswanadham Sridhara wrote: > Hello gmx users, > > Were there any previous molecular dynamics simulations done on > cardiolipin / Cytochrome C binding? Dunno. There's no substitute for searching the literature. > Any "pdb" files available for either Cardiolipin or cytochrome C,. any > literature available / any tutorials. Dunno. Looking in the Protein Databank would be more profitable for you. http://www.rcsb.org/pdb/ Mark From g.groenhof at rug.nl Fri Sep 29 00:37:50 2006 From: g.groenhof at rug.nl (Gerrit Groenhof) Date: Fri, 29 Sep 2006 00:37:50 +0200 Subject: [gmx-users] QMMM interface In-Reply-To: <20060928140131.i1nk3bcu6g408c4c@webmail.ufp.pt> References: <20060928140131.i1nk3bcu6g408c4c@webmail.ufp.pt> Message-ID: <1957a4ade48659357f90c4280d3b2856@rug.nl> It does not exist, but since gmx is open source, I suggest you give it a try. I suppose the input/output is similar to gamess-uk? In that case, have a look at mdlib/qmmm.c and gamess.c. Contact me off list at ggroenh<>gwdg.de if you need more help. Gerrit On Sep 28, 2006, at 3:01 PM, pedros at ufp.pt wrote: > > Dear Gromacs users, > > I have been using Pcgamess for QM calculations, which is a very fast > (and free) program, and has some QMMM capabilities(but a size limit of > about 1000 atoms ). I just found out that Gromacs now has QMMM > capabilities with CPMD, Gaussian and Gamess(UK). Does any one know > whether a Gromacs-PcGamess QMMM interface is planned? It would be > great for those of us with small research budgets, and who cannot > afford the comercial QM codes. > > Pedro > > ---------------------------------------------------------------- > Enviado por https://webmail.ufp.pt > > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > Note, from 2005 on my email adress has changed to ggroenh at gwdg.de From toma0052 at umn.edu Fri Sep 29 03:11:58 2006 From: toma0052 at umn.edu (toma0052) Date: Thu, 28 Sep 2006 20:11:58 CDT Subject: [gmx-users] Lipid Bilayer Simulations Message-ID: <200609290111.k8T1BwfJ005196@vendetta.software.umn.edu> Hi, I am new to Gromacs, and I am working with lipid bilayer simulations. I am attempting to just run an energy minimization on a lipid bilayer so I can get a better feel for the program. I have taken the files dppc128.pdb, dppc.itp, lipid.itp and example2.itp from Peter Tieleman's website. Because I could not use teh pdb2gmx command, I started with the editconf command and then the genbox command, both of which seemed to run successfully. Then, I tried to do the preprocessing with the grompp command, but I received the error; Fatal Error: Found a second defaults directive, file "lipid.itp". When I removed lipid.itp from the topology file, I received the error; Fatal Error: Atomtype 'LC3' not found! As I said before, I am new to Gromacs, and I am not sure how to get around this problem. Do I need to put the dppc.itp and lipid.itp file together into one? Any help would be appreciated. Thanks, Mike Tomasini From anwar at cdfd.org.in Fri Sep 29 12:28:11 2006 From: anwar at cdfd.org.in (anwar at cdfd.org.in) Date: Fri, 29 Sep 2006 03:28:11 -0700 (PDT) Subject: [gmx-users] defining 2 posres at a time in mdp Message-ID: <19979806.1159496124208.JavaMail.nobody@sunserver> hi all, I want to define position restraints for a part of protein and water molecules also. I need to deinfe -DPOSRES and -DPOSRES_WATER at the same time. When I do it on separate lines in the mdp file, only first line is being read and accepted. Is there any way to include both of them in the same mdp file simultaneously. regards anwar - From dennis at iitk.ac.in Fri Sep 29 08:00:39 2006 From: dennis at iitk.ac.in (Dilraj Lama) Date: Fri, 29 Sep 2006 11:30:39 +0530 (IST) Subject: [gmx-users] defining 2 posres at a time in mdp In-Reply-To: <19979806.1159496124208.JavaMail.nobody@sunserver> References: <19979806.1159496124208.JavaMail.nobody@sunserver> Message-ID: <53438.172.28.124.10.1159509639.squirrel@newwebmail.iitk.ac.in> define them in the same line. define = -DPOSRES_WATER -DPOSRES > hi all, > I want to define position restraints for a part of protein and water > molecules > also. I need to deinfe -DPOSRES and -DPOSRES_WATER at the same time. When > I do it on separate lines in the mdp file, only first line is being read > and accepted. Is there any way to include both of them in the same mdp > file simultaneously. > regards > anwar > - > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Dilraj Lama, Graduate student, Bioinformatics and Biomolecular Simualtion lab, Dept. of BSBE;IITK-kanpur, Uttar pradesh,India-208016. email:dennis at iitk.ac.in,dilraj2002 at yahoo.com mob:09415473973 From zgxjlx at gmail.com Fri Sep 29 10:11:26 2006 From: zgxjlx at gmail.com (liu xin) Date: Fri, 29 Sep 2006 16:11:26 +0800 Subject: [gmx-users] HBond frequency Message-ID: Hello GMX users: Just a quick question: how can I get the frequency of each HBond? >From hbond.ndx we can get a list of hbonds, e.g. hbonds between protein and drug, if I want to check the frequency of each hbond between the two components respectively, how can I realize it? -------------- next part -------------- An HTML attachment was scrubbed... URL: From Mark.Abraham at anu.edu.au Fri Sep 29 10:28:18 2006 From: Mark.Abraham at anu.edu.au (Mark Abraham) Date: Fri, 29 Sep 2006 18:28:18 +1000 Subject: [gmx-users] HBond frequency In-Reply-To: References: Message-ID: <451CD922.9030901@anu.edu.au> liu xin wrote: > Hello GMX users: > > Just a quick question: how can I get the frequency of each HBond? > > From hbond.ndx we can get a list of hbonds, e.g. hbonds between protein > and drug, if I want to check the frequency of each hbond between the two > components respectively, how can I realize it? man g_hbond and look for -xbm Mark From anoddlad at yahoo.com Fri Sep 29 13:12:18 2006 From: anoddlad at yahoo.com (Alan Dodd) Date: Fri, 29 Sep 2006 04:12:18 -0700 (PDT) Subject: [gmx-users] Lipid Bilayer Simulations In-Reply-To: <200609290111.k8T1BwfJ005196@vendetta.software.umn.edu> Message-ID: <20060929111218.96240.qmail@web39112.mail.mud.yahoo.com> Configuring the .itp files etc initially is a bit tricksy without knowing what you're doing, the short not-very-helpful answer is "read the manual". There's a whole chapter (5?) on forcefield files and their formats. It's entirely possible to set it all up so that pdb2gmx does in fact work, but to do this you need to edit the forcefield files in the main gromacs folder for these things (add your lipid.itp and dppc.itp, add "#include" for each of these to your forcefield of choice). Anyways: I'd guess it was complaining initially because #include files were in the wrong order in your .top, and then subsequently because you removed the reference to lipid.itp (which you need). Unless someone can be of more help, I suggest you just tinker. --- toma0052 wrote: > Hi, > I am new to Gromacs, and I am working with > lipid bilayer simulations. > I am attempting to just run an energy minimization > on a lipid bilayer so I > can get a better feel for the program. I have taken > the files dppc128.pdb, > dppc.itp, lipid.itp and example2.itp from Peter > Tieleman's website. > Because I could not use teh pdb2gmx command, I > started with the editconf > command and then the genbox command, both of which > seemed to run > successfully. Then, I tried to do the preprocessing > with the grompp > command, but I received the error; Fatal Error: > Found a second defaults > directive, file "lipid.itp". When I removed > lipid.itp from the topology > file, I received the error; Fatal Error: Atomtype > 'LC3' not found! As I > said before, I am new to Gromacs, and I am not sure > how to get around this > problem. Do I need to put the dppc.itp and lipid.itp > file together into > one? Any help would be appreciated. > > Thanks, > Mike Tomasini > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the > list. Use the > www interface or send it to > gmx-users-request at gromacs.org. > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From mollica.luca at hsr.it Fri Sep 29 13:48:20 2006 From: mollica.luca at hsr.it (Luca Mollica) Date: Fri, 29 Sep 2006 13:48:20 +0200 Subject: [gmx-users] Zn ion as a metal center in a protein: setting distance restraints Message-ID: <451D0804.7090604@hsr.it> Dear all, I have tried to simulate my protein-ligand system in water as usual, but my protein has two Zn atoms that bind 3Cys and 1 His (Zn1) and 4Cys (Zn2). I have browsed the literature and the ML: the most common suggestion that I had found was the usage of distance restraints in my protein topology file. After a bit of manual reading, I have set up my table for distance restraints as follows: [distance restraints] 620 98 1 0 1 0.18 0.30 0.35 1 ;Zn1 - His 620 120 1 0 1 0.18 0.30 0.35 1 ;Zn1 - Cys1 620 278 1 0 1 0.18 0.30 0.35 1 ;Zn1 - Cys2 620 304 1 0 1 0.18 0.30 0.35 1 ;Zn1 - Cys3 621 479 1 1 1 0.18 0.30 0.35 1 ;Zn2 - Cys4 621 222 1 1 1 0.18 0.30 0.35 1 ;Zn2 - Cys5 621 200 1 1 1 0.18 0.30 0.35 1 ;Zn2 - Cys6 621 455 1 1 1 0.18 0.30 0.35 1 ;Zn2 - Cys7 and the options used in the mdp file were: disre = simple disre_fc = 4000 disre_weighting = equal I have noticed that, with respect to the first simulation that I had set up without distance restraints (just a mistake) I do not see my two Zn atoms floating in solution like counterions or water molecules. Neverthless, I am not really happy of the result I got: indeed, the second Zn atom (indexd with 1) is more or less stable in its coordination pocket (Zn-S distance ~4-5 A), whereas the first Zn atom (indexed with 0) is really strongly bound to Nd1 but it is not in the right coordination, being the distance between Zn and Cys S atoms ~ 7-8 Angstrom. Do you have any suggestion about how to get an improvement in my simulations ? Moreover, do you think that the distance restraints table is badly written and/or does it contain errors ? My desire is to use a distance restraints table that allows distance (without penalty) between 1.8 A and 3.5 A, which are the same restraints tha have been used for structure determination by NMR (using CYANA). Thanx a lot for any help All the best Luca ******************************************************************** Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi ("Ricerca sanitaria") il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a 5permille at hsr.it o vai sul sito www.5xmille.org From qiaobf at gmail.com Fri Sep 29 14:19:41 2006 From: qiaobf at gmail.com (Qiao Baofu) Date: Fri, 29 Sep 2006 14:19:41 +0200 Subject: [gmx-users] question about energy and pressure In-Reply-To: <45137A13.3090809@anu.edu.au> References: <6a91f07b0609200513g5c404d49gd5e5e8f784afd0b6@mail.gmail.com> <45137A13.3090809@anu.edu.au> Message-ID: <6a91f07b0609290519i1ffbfb2fh7b43e7e65ba5bbb9@mail.gmail.com> Hi Mark, 2006/9/22, Mark Abraham : > > Qiao Baofu wrote: > > What is this "reported data"? The reported data are (KJ/mol) : Bond 27; Angle: 30; LJ: -27; electrostatic -530. Some days ago, I run again in gromacs but using all the "reported" force-field parameters. In the end, I get the similar result as listed in the first letter. Have someone compared the energy of gromacs with other software? > Statistics over 5000001 steps [ 0.0000 thru 5000.0000 ps ], 6 data sets > > > > Energy Average RMSD Fluct. Drift > > Tot-Drift > > > ------------------------------------------------------------------------------- > > > > Bond 2869.13 93.6564 93.6562 0.000137548 > > 0.687742 > > Angle 7303.46 140.13 140.13 0.000189867 > > 0.949334 > > Ryckaert-Bell. 3326.2 97.6245 97.6161 -0.000890977 - > 4.45489 > > LJ-(SR) -7616.62 138.684 138.67 -0.00138166 > > -6.90831 > > Coulomb-(SR) -22763.2 138.465 138.238 -0.00549019 - > 27.451 > > Potential -64743 219.54 219.203 -0.00842365 > > -42.1182 > > > > 2. I used the "isotropic!!" pressure coupling, but at the end of the > > .log file (in the average section), it says: > > > > Pressure (bar) > > -2.64364e+01 3.71622e+01 3.00738e+00 > > 3.71622e+01 1.32932e+01 -2.49814e+01 > > 3.00738e+00 -2.49814e+01 1.61609e+01 > > > > The Pxx, Pyy, Pzz are not equal. Why? > > What is the geometry of your system? It is imidazolium-based material. PS: The following processes are used: 1. md1: NTV (nose-hoover for T coupling) 300ps 2. md2: NTP (Berendsen for T & P coupling) T=425K, P=1bar, 500ps, tau_p=1 3. in md3.mdp: gen_temp = no unconstrained-start = yes grompp -e md2.edr -f md3.mdp -c md2.gro -p -o md3: NTP (nose-hoover for T coupling & Parrillo-rahman for P coupling) T=425K, P=1bar, 3000ps, tau_p=4 4. collect data. g_energy Energy Average RMSD Fluct. Drift Tot-Drift ------------------------------------------------------------------------------- Pressure-(bar) 1.75443 931.231 931.227 -0.00331938 - 9.95814 In md3.log Pressure (bar) 3.37452e+01 -1.01961e+02 1.77413e+01 -1.01961e+02 -7.66155e+00 -4.13047e+01 1.77413e+01 -4.13047e+01 -2.08203e+01 Even though I used the Berendsen P coupling to relax the pressure firstly, and then use the Parrilo-rahman, the final result of pressure deviates much from what I want! After md2 and md3, I both used g_velacc to check the velocity-corelation function. Who has such experience? How to solve it? Mark > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Sincerely yours, ********************************************** Baofu Qiao, PhD Frankfurt Institute for Advanced Studies Max-von-Laue-Str. 1 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From jon.ellis at utoronto.ca Fri Sep 29 16:29:28 2006 From: jon.ellis at utoronto.ca (Jon Ellis) Date: Fri, 29 Sep 2006 10:29:28 -0400 Subject: [gmx-users] g_traj -ng not working with option -ng Message-ID: <626B690C-9920-4E4C-9BFB-9192C5948193@utoronto.ca> Hello GMXers I am trying to extract coordinates for a number of different groups over a trajectory using g_traj. When I run g_traj with the -ng 16 option, I can only specify a single group. I've tried for fewer or more groups, with no success, and I've tested to see if it would ask for the next group when it was finished, but it didn't. It works fine when I use -com, but I need the full coordinates, not just Centres of Mass. I could specify each single atom as a group, but that would further increase the number of groups, and the post- processing, so I'm wondering if there's a solution? I'm running v3.3, but I've tried it with 3.31 as well. Any hints? Cheers Jon Ellis ---------------------------------------- Jon Ellis PhD Candidate, Thompson Group Institute of Biomaterials and Biomedical Engineering/Dept of Chemistry University of Toronto Lash Miller 147 (416) 978-6568 jon.ellis at utoronto.ca ---------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From JMoore2 at dow.com Fri Sep 29 17:42:44 2006 From: JMoore2 at dow.com (Moore, Jonathan (J)) Date: Fri, 29 Sep 2006 11:42:44 -0400 Subject: [gmx-users] g_traj -ng not working with option -ng Message-ID: <36CED4C6D1D4FB4EAD8CFE68BCFCE4EC06F51E@USMDLMDOWX022.dow.com> I submitted this as a bug a few days ago... bug 107 http://bugzilla.gromacs.org/show_bug.cgi?id=107 Thanks, Jonathan ____________________________ Jonathan Moore, Ph.D. Research and Engineering Sciences - New Products Core R&D The Dow Chemical Company 1702 Building, Office 300E Midland, MI 48674 USA Phone: (989) 636-9765 Fax: (989) 636-4019 E Mail: jmoore2 at dow.com -----Original Message----- From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Jon Ellis Sent: Friday, September 29, 2006 10:29 AM To: gmx-users at gromacs.org Subject: [gmx-users] g_traj -ng not working with option -ng Hello GMXers I am trying to extract coordinates for a number of different groups over a trajectory using g_traj. When I run g_traj with the -ng 16 option, I can only specify a single group. I've tried for fewer or more groups, with no success, and I've tested to see if it would ask for the next group when it was finished, but it didn't. It works fine when I use -com, but I need the full coordinates, not just Centres of Mass. I could specify each single atom as a group, but that would further increase the number of groups, and the post-processing, so I'm wondering if there's a solution? I'm running v3.3, but I've tried it with 3.31 as well. Any hints? Cheers Jon Ellis ---------------------------------------- Jon Ellis PhD Candidate, Thompson Group Institute of Biomaterials and Biomedical Engineering/Dept of Chemistry University of Toronto Lash Miller 147 (416) 978-6568 jon.ellis at utoronto.ca ---------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From mollica.luca at hsr.it Fri Sep 29 18:28:54 2006 From: mollica.luca at hsr.it (Luca Mollica) Date: Fri, 29 Sep 2006 18:28:54 +0200 Subject: [gmx-users] Lipid Bilayer Simulations Message-ID: <451D49C6.7010904@hsr.it> Hi Mike! > I am new to Gromacs, and I am working with > lipid bilayer simulations. > I am attempting to just run an energy minimization > on a lipid bilayer so I > can get a better feel for the program. I have taken > the files dppc128.pdb, > dppc.itp, lipid.itp and example2.itp from Peter > Tieleman's website. > Because I could not use teh pdb2gmx command, I > started with the editconf > command and then the genbox command, both of which > seemed to run > successfully. Then, I tried to do the preprocessing actually, in this way you are more or less editing your files and adding some solvent molecules, nothing to do with FF & top/itp files related to lipid molecules ... > with the grompp > command, but I received the error; Fatal Error: > Found a second defaults > directive, file "lipid.itp". When I removed > lipid.itp from the topology > file, I received the error; Fatal Error: Atomtype Mm, ok ... I think you have two different solutions you can try: 1. Download from the website of GROMACS http://www.gromacs.org/contributed_by_users/task,cat_view/gid,37/ a FF that is modified according to parameters describing lipids: I personally have inserted in my installation /usr/local/share/top (or whetheaver) directory these files and everything is working fine (both with 3.2 and 3.3 versions of GMX). In this way everything is included in the default FF and path in your machine. In case you do not have any access to your root directory and you are not the machine administrator, do not worry: insert all these untarred files in your working dir and everything will be fine! In this way you won'need any longer lipid.itp file for the used FF. 2. The second solution could simply be the usage of #include "lipid.itp" before #include "dppc.itp" in the topology file as suggested in the other reply. > 'LC3' not found! As I > said before, I am new to Gromacs, and I am not sure That's the point ! Actually GROMACS does not know who this guy is .... ;) Cheers and have nice MD on biomembranes Luca ******************************************************************** Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi ("Ricerca sanitaria") il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a 5permille at hsr.it o vai sul sito www.5xmille.org From JMoore2 at dow.com Fri Sep 29 21:30:24 2006 From: JMoore2 at dow.com (Moore, Jonathan (J)) Date: Fri, 29 Sep 2006 15:30:24 -0400 Subject: [gmx-users] g_traj -ng not working with option -ng Message-ID: <36CED4C6D1D4FB4EAD8CFE68BCFCE4EC06F51F@USMDLMDOWX022.dow.com> By the way, another way to get the coordinates out is to use trjconv to read a .xtc (or whatever) and output a .gro (for example). Thanks, Jonathan ____________________________ Jonathan Moore, Ph.D. Research and Engineering Sciences - New Products Core R&D The Dow Chemical Company 1702 Building, Office 300E Midland, MI 48674 USA Phone: (989) 636-9765 Fax: (989) 636-4019 E Mail: jmoore2 at dow.com -----Original Message----- From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Jon Ellis Sent: Friday, September 29, 2006 10:29 AM To: gmx-users at gromacs.org Subject: [gmx-users] g_traj -ng not working with option -ng Hello GMXers I am trying to extract coordinates for a number of different groups over a trajectory using g_traj. When I run g_traj with the -ng 16 option, I can only specify a single group. I've tried for fewer or more groups, with no success, and I've tested to see if it would ask for the next group when it was finished, but it didn't. It works fine when I use -com, but I need the full coordinates, not just Centres of Mass. I could specify each single atom as a group, but that would further increase the number of groups, and the post-processing, so I'm wondering if there's a solution? I'm running v3.3, but I've tried it with 3.31 as well. Any hints? Cheers Jon Ellis ---------------------------------------- Jon Ellis PhD Candidate, Thompson Group Institute of Biomaterials and Biomedical Engineering/Dept of Chemistry University of Toronto Lash Miller 147 (416) 978-6568 jon.ellis at utoronto.ca ---------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From erikm at xray.bmc.uu.se Sat Sep 30 02:46:03 2006 From: erikm at xray.bmc.uu.se (Erik Marklund) Date: Fri, 29 Sep 2006 17:46:03 -0700 Subject: [gmx-users] HBond frequency References: <451CD922.9030901@anu.edu.au> Message-ID: <002601c6e429$d13f0c80$c6c011ac@Katten> ----- Original Message ----- From: "Mark Abraham" To: "Discussion list for GROMACS users" Sent: Friday, September 29, 2006 1:28 AM Subject: Re: [gmx-users] HBond frequency > liu xin wrote: >> Hello GMX users: >> >> Just a quick question: how can I get the frequency of each HBond? >> >> From hbond.ndx we can get a list of hbonds, e.g. hbonds between protein >> and drug, if I want to check the frequency of each hbond between the two >> components respectively, how can I realize it? > > man g_hbond and look for -xbm Almost. -hbm is the flag you would want to use. /Erik > > Mark > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > From zgxjlx at gmail.com Sat Sep 30 09:09:28 2006 From: zgxjlx at gmail.com (liu xin) Date: Sat, 30 Sep 2006 15:09:28 +0800 Subject: [gmx-users] HBond frequency In-Reply-To: <002601c6e429$d13f0c80$c6c011ac@Katten> References: <451CD922.9030901@anu.edu.au> <002601c6e429$d13f0c80$c6c011ac@Katten> Message-ID: Thanks, but when ever I used ACDsee to visualize the generated hbmap.xpm, I've got nothing, and ACDsee keeps on telling me that "Bad or unrecognized image header". On 9/30/06, Erik Marklund wrote: > > > ----- Original Message ----- > From: "Mark Abraham" > To: "Discussion list for GROMACS users" > Sent: Friday, September 29, 2006 1:28 AM > Subject: Re: [gmx-users] HBond frequency > > > > liu xin wrote: > >> Hello GMX users: > >> > >> Just a quick question: how can I get the frequency of each HBond? > >> > >> From hbond.ndx we can get a list of hbonds, e.g. hbonds between > protein > >> and drug, if I want to check the frequency of each hbond between the > two > >> components respectively, how can I realize it? > > > > man g_hbond and look for -xbm > > Almost. -hbm is the flag you would want to use. > > /Erik > > > > > Mark > > _______________________________________________ > > gmx-users mailing list gmx-users at gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the www > > interface or send it to gmx-users-request at gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -------------- next part -------------- An HTML attachment was scrubbed... URL: From spoel at xray.bmc.uu.se Sat Sep 30 11:37:47 2006 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Sat, 30 Sep 2006 11:37:47 +0200 Subject: [gmx-users] HBond frequency In-Reply-To: References: <451CD922.9030901@anu.edu.au> <002601c6e429$d13f0c80$c6c011ac@Katten> Message-ID: <451E3AEB.6010807@xray.bmc.uu.se> liu xin wrote: > Thanks, but when ever I used ACDsee to visualize the generated > hbmap.xpm, I've got nothing, and ACDsee keeps on telling me that "Bad or > unrecognized image header". > Try the gimp or use xpm2ps first. -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From erikm at xray.bmc.uu.se Sat Sep 30 18:26:12 2006 From: erikm at xray.bmc.uu.se (Erik Marklund) Date: Sat, 30 Sep 2006 09:26:12 -0700 Subject: [gmx-users] HBond frequency References: <451CD922.9030901@anu.edu.au><002601c6e429$d13f0c80$c6c011ac@Katten> <451E3AEB.6010807@xray.bmc.uu.se> Message-ID: <002001c6e4ad$28a7d280$c6c011ac@Katten> ----- Original Message ----- From: "David van der Spoel" To: "Discussion list for GROMACS users" Sent: Saturday, September 30, 2006 2:37 AM Subject: Re: [gmx-users] HBond frequency > liu xin wrote: >> Thanks, but when ever I used ACDsee to visualize the generated hbmap.xpm, >> I've got nothing, and ACDsee keeps on telling me that "Bad or >> unrecognized image header". >> > Try the gimp or use xpm2ps first. > > -- > David. Or analyze the data by other means. The image data is uncompressed and stored row-wise in the file, making it relatively easy to extract, in your case, hbond frequencies, using most any scripting language. /Erik > ________________________________________________________________________ > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > From erikm at xray.bmc.uu.se Sat Sep 30 18:26:12 2006 From: erikm at xray.bmc.uu.se (Erik Marklund) Date: Sat, 30 Sep 2006 09:26:12 -0700 Subject: [gmx-users] HBond frequency References: <451CD922.9030901@anu.edu.au><002601c6e429$d13f0c80$c6c011ac@Katten> <451E3AEB.6010807@xray.bmc.uu.se> Message-ID: <002001c6e4ad$28a7d280$c6c011ac@Katten> ----- Original Message ----- From: "David van der Spoel" To: "Discussion list for GROMACS users" Sent: Saturday, September 30, 2006 2:37 AM Subject: Re: [gmx-users] HBond frequency > liu xin wrote: >> Thanks, but when ever I used ACDsee to visualize the generated hbmap.xpm, >> I've got nothing, and ACDsee keeps on telling me that "Bad or >> unrecognized image header". >> > Try the gimp or use xpm2ps first. > > -- > David. Or analyze the data by other means. The image data is uncompressed and stored row-wise in the file, making it relatively easy to extract, in your case, hbond frequencies, using most any scripting language. /Erik > ________________________________________________________________________ > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >