[gmx-users] Re: gmx-users Digest, Vol 60, Issue 116
nitu sharma
sharmanitu35 at gmail.com
Thu Apr 23 11:24:47 CEST 2009
On Thu, Apr 23, 2009 at 11:55 AM, <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. Re: np command with GROMACS 4.0.4 (Vitaly V. Chaban)
> 2. Re: RMSD of Aminoacids (Mark Abraham)
> 3. problem in topology file of protein-lipid bilayer system for
> grompp (nitu sharma)
> 4. validating gromacs installation 4.0.4 ( Y. U. Sasidhar )
> 5. Re: problem in topology file of protein-lipid bilayer system
> for grompp (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 22 Apr 2009 22:36:51 +0200
> From: "Vitaly V. Chaban" <vvchaban at gmail.com>
> Subject: [gmx-users] Re: np command with GROMACS 4.0.4
> To: gmx-users at gromacs.org
> Message-ID:
> <7138ee40904221336u626133d5mdcf42f1b47e70acd at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> If seems in the gmx versions above 4.0 '-np' is not used. If I am not
> mistaken you should just point out the number of nodes in your queueing
> system while submitting the job.
>
> Vitaly
>
>
> > I am trying to do my position restrained dynamic simulation on GROMACS
> > 4.0.4, and I want to use 4 nodes on the cpu cluster available at my
> campus;
> > I typed in the following grompp command:
> >
> > grompp -np 4 -f pr.mdp -c BR6_em.pdb -p BR6.top -o BR6_pr.tpr -n prot.ndx
> > -maxwarn 10
> >
> > and it gave me the response that -np is an invalid command.
> >
> > How do I get grompp to rec. that I want to use 4 processors? Because my
> > job
> > script where I have specified 4 nodes, will not work unless I have np 4
> > included in my grompp. I did see that it works with GROMACS 3.3.3...but
> is
> > there a way to do it with 4.0.4?
> >
> > Thanks so much!
> >
> > Halie Shah
> > University of Houston, TX U.S.
> > Briggs Lab
> >
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://www.gromacs.org/pipermail/gmx-users/attachments/20090422/363187da/attachment-0001.html
>
> ------------------------------
>
> Message: 2
> Date: Thu, 23 Apr 2009 10:04:36 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] RMSD of Aminoacids
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <49EFB094.9040908 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Andy Torres wrote:
> > Hi, I'm trying to compare two proteins with the same number of
> > aminoacids with g_confrms, and it works all right, but it gives me the
> > RMSD of the hole protein, and I need the distances (or deviations) of
> > each aminoacid. I know this data shoul be there, but I don't know how to
> > get it (I've got the mean structure of each protein, calculated with
> > g_rmsf, but this data is not fitted each other)
>
> Have a look at g_confrms -h. Probably with the right index groups
> constructed you can fit with one group and observe the RMSD with another.
>
> Mark
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 23 Apr 2009 10:31:10 +0530
> From: nitu sharma <sharmanitu35 at gmail.com>
> Subject: [gmx-users] problem in topology file of protein-lipid bilayer
> system for grompp
> To: gmx-users at gromacs.org
> Message-ID:
> <5fe39aa90904222201n7e5181c4p87111ffd86958741 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Justin
>
> I am doing simulation of membrane protein .I
> follow your tutorial for that I think its perfect for that. But I am
> getting
> problem in doing inflategro step, I alredy discuss this problem with you
> but
> now I am starting everything fresh I have completed upto concatanation of
> protein with lipid bilayer after that for packing of lipid around protein I
> am using inflategro script from teleman website . Problem came in second
> step of inflategro i.e for energy minimisation for this I need topology
> file
> of "protein-lipid system".
> I am giving you information in detail i.e -
> for topology file I have made changes in topol.top file which I got from
> pdb2gmx command in first step for protein processing ,the topol .top file
> is
> like this-
> File 'topol.top' was generated
> ; By user: nitu (504)
> ; On host: localhost.localdomain
> ; At date: Thu Apr 16 23:20:48 2009
> ;
> ; This is your topology file
> ; Grunge ROck MAChoS
> ;
> ; Include forcefield parameters
> #include "ffG53a6.itp"
>
> ; Include chain topologies
> #include "topol_A.itp"
> #include "topol_B.itp"
>
> ; Include water topology
> #include "spc.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> #endif
>
> ; Include generic topology for ions
> #include "ions.itp"
>
> [ system ]
> ; Name
> Grunge ROck MAChoS
>
> [ molecules ]
> ; Compound #mols
> Protein_A 1
> Protein_B 1
> **********
> And the change topology file is like this-
>
> ; Include forcefield parameters
> #include "ffG53a6_lipid.itp"
>
> ; Include chain topologies
> #include "topol_A.itp"
> #include "topol_B.itp"
>
> #ifdef POSRES
> #include "posre_A.itp"
> #include "posre_B.itp"
> #endif
>
> ; Include DMPC chain topology
> #include "dmpc.itp"
>
>
> [ system ]
> ; Name
> Protein in DMPC bilayer
>
> [ molecules ]
> ; Compound #mols
> Protein_A 1
> Protein_B 1
> DMPC 128
>
> but when I gave this topology file to grompp it shws error-
> no. of coordinates in coordinate file doesn,t mach the topology file .
>
> Can you suggest me something for making topology file for protein-lipid
> bilayer system. Is there any other method for making topology file ,I have
> read in mannual chapter 5 but there is also mentioned same method.
> If possible please help me becoz without solving this problem I can't move
> for furthur processing .
>
> * My gro file of protein shows 9902 atoms .
> As you ask in previous mail is .itp file have [ molecules ] section the
> answer is the .itp file haven't molecules section it have [molecule type ]
> section can it also create problem for topology file working.
>
> Thanks a lot justin .
> I am waiting for your reply.
>
> Nitu sharma
> School of life sciences
> Jawaherlal Nehru University
> New delhi , India
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://www.gromacs.org/pipermail/gmx-users/attachments/20090423/45256e1c/attachment-0001.html
>
> ------------------------------
>
> Message: 4
> Date: Thu, 23 Apr 2009 10:53:13 +0530
> From: " Y. U. Sasidhar " <sasidhar at chem.iitb.ac.in>
> Subject: [gmx-users] validating gromacs installation 4.0.4
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <49EFFB41.3060204 at chem.iitb.ac.in>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Dear Users, I posted the following message a few days ago; So far I have
> not got any response. Searching archives also seem to indicate that
> people are facing similar problems. Some times modifying mdp options
> make the tests "pass" as we also observed ( see below ).
>
> Further the reference trajectories seem to be generated by versions
> 3.2/3.3.
>
> Are there reference trajectories for 4.0.4?
>
> If some of the tests "fail", does it mean gromacs is not computing as it
> should? the results can not be relied on?
>
> As of now numbers are compared to test pass/failure.
>
> Can physical properties - like rdf of spc water, diffusion constants
> etc- be used to test gromacs?
>
> I thank you very much for your time.
>
> The "failures" are presenting a dilemma. I hope I have done what I can
> as a user and hope to resolve the issue with your help.
>
> regards,
>
> Sasidhar
>
> PS: we notice that with double precision failures are less; further with
> version 3.2 the failures are less suggesting that numerical accuracies
> of machines, differences in algorithms, if any, used in different
> versions could be a cause for "failures"
> ==============previously posted message=============
>
>
>
> Dear users,
>
> We have installed gmx 4.0.4 ( single precision, on cent os 4.3 ( 32 bit
> ) on quad core dual xeon machine ( clock 2 GHz )
>
> Installation directions as given on the site followed.
> And the tests are run using the perl script provided plus test
> files/folders.
>
> We find many failures ( see below ); However, by changing mdp options
> all the tests "passed" as detailed below. For example, for the "field"
> test coulomb type changed to PME and the test passes with this change.
>
> The implication is that reference trajectory computed using cut-off
> "matches" with newly calculated trajectory using more accurate PME
> method. You can see more details below. **So did the tests really pass?**
>
> We understand energies, virials and forces are compared for all tests to
> report errors/failures.
>
>
> When we searched archives we did not find clear solutions to
> test-failure-problems. Wiki site does not give any further guidance.
> We have looked at wiki site.
>
> In the presence of failures it is not clear how to proceed further.
>
> Kindly guide us in upgrading to gmx 4.04 and "clearing" the tests.
> regards,
> Sasidhar
>
>
>
>
>
> ==========================================================================
> This is the output (before making any changes), when i get when i run the
> test script gmxtest.pl for 4.0.4 on gromacs-4.0.4.
>
> $ ./gmxtest.pl all
> All 16 simple tests PASSED
> FAILED. Check files in field
> FAILED. Check files in tip4p
> FAILED. Check files in tip4pflex
> FAILED. Check files in water
> 4 out of 14 complex tests FAILED
> FAILED. Check files in kernel020
> FAILED. Check files in kernel120
> FAILED. Check files in kernel121
> FAILED. Check files in kernel122
> FAILED. Check files in kernel123
> FAILED. Check files in kernel124
> FAILED. Check files in kernel220
> FAILED. Check files in kernel221
> FAILED. Check files in kernel222
> FAILED. Check files in kernel223
> FAILED. Check files in kernel224
> FAILED. Check files in kernel320
> FAILED. Check files in kernel321
> FAILED. Check files in kernel322
> FAILED. Check files in kernel323
> FAILED. Check files in kernel324
> 16 out of 63 kernel tests FAILED
> N Reference This test
> 10 -33.9883 -29.4637
> 11 -33.9883 -29.4637
> There were 2 differences in final energy with the reference file
> All 45 pdb2gmx tests PASSED
> pdb2gmx tests FAILED
>
>
> The tests which failed previously, passed when following changes were made
> to the grompp.mdp files of the failed test directories.
>
> 1) field : coulombtype : cut-off to PME
> 2) tip4p : tempcoupl : berendsen to V-rescale
> 3) tip4pflex : vdwtype : cut-off to shift
> 4) water : tempcoupl : yes to V-rescale
>
> 5)kernel020-124 : coulombtype : cut-off to PME & making rlist = rcoulomb
> 6)kernel220-224 : coulombtype : recation-field-nec to PME & making rlist =
> rcoulomb
>
> 7)kernel320-324 : coulombtype : switch to PME & making rlist = rcoulomb.
>
>
>
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 23 Apr 2009 16:24:39 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] problem in topology file of protein-lipid
> bilayer system for grompp
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <49F009A7.9090108 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> nitu sharma wrote:
> > Dear Justin
> >
> > I am doing simulation of membrane protein .I
> > follow your tutorial for that I think its perfect for that. But I am
> > getting problem in doing inflategro step, I alredy discuss this problem
> > with you but now I am starting everything fresh I have completed upto
> > concatanation of protein with lipid bilayer after that for packing of
> > lipid around protein I am using inflategro script from teleman website
> > . Problem came in second step of inflategro i.e for energy minimisation
> > for this I need topology file of "protein-lipid system".
> > I am giving you information in detail i.e -
> > for topology file I have made changes in topol.top file which I got from
> > pdb2gmx command in first step for protein processing ,the topol .top
> > file is like this-
> > File 'topol.top' was generated
> > ; By user: nitu (504)
> > ; On host: localhost.localdomain
> > ; At date: Thu Apr 16 23:20:48 2009
> > ;
> > ; This is your topology file
> > ; Grunge ROck MAChoS
> > ;
> > ; Include forcefield parameters
> > #include "ffG53a6.itp"
> >
> > ; Include chain topologies
> > #include "topol_A.itp"
> > #include "topol_B.itp"
> >
> > ; Include water topology
> > #include "spc.itp"
> >
> > #ifdef POSRES_WATER
> > ; Position restraint for each water oxygen
> > [ position_restraints ]
> > ; i funct fcx fcy fcz
> > 1 1 1000 1000 1000
> > #endif
> >
> > ; Include generic topology for ions
> > #include "ions.itp"
> >
> > [ system ]
> > ; Name
> > Grunge ROck MAChoS
> >
> > [ molecules ]
> > ; Compound #mols
> > Protein_A 1
> > Protein_B 1
> > **********
> > And the change topology file is like this-
> >
> > ; Include forcefield parameters
> > #include "ffG53a6_lipid.itp"
> >
> > ; Include chain topologies
> > #include "topol_A.itp"
> > #include "topol_B.itp"
> >
> > #ifdef POSRES
> > #include "posre_A.itp"
> > #include "posre_B.itp"
> > #endif
>
> I think you've been told before that this is garbage.
> [position_restraints] directives are components of a [moleculetype], and
> so must come before the [moleculetype] of a subsequent molecule. Your
> use of the last four #include preprocessing commands violates this. You
> should make two #ifdef POSRES sections appropriately.
>
> > ; Include DMPC chain topology
> > #include "dmpc.itp"
> >
> >
> > [ system ]
> > ; Name
> > Protein in DMPC bilayer
> >
> > [ molecules ]
> > ; Compound #mols
> > Protein_A 1
> > Protein_B 1
> > DMPC 128
> >
> > but when I gave this topology file to grompp it shws error-
> > no. of coordinates in coordinate file doesn,t mach the topology file .
>
> OK, so do the arithmetic and see what the problem is.
>
> > Can you suggest me something for making topology file for protein-lipid
> > bilayer system. Is there any other method for making topology file ,I
> > have read in mannual chapter 5 but there is also mentioned same method.
> > If possible please help me becoz without solving this problem I can't
> > move for furthur processing .
> >
> > * My gro file of protein shows 9902 atoms .
> > As you ask in previous mail is .itp file have [ molecules ] section the
> > answer is the .itp file haven't molecules section it have [molecule type
> > ] section can it also create problem for topology file working.
>
> So you have 9902 atoms in your coordinate file. How many atoms are in
> protein A, protein B and the 128 copies of DMPC *according to their
> [moleculetype] definitions*?
>
> Mark
Dear Mark
Thanks for your reply. as u ask- how many atoms is------Protein A- 5244
protein B- 4658
And in one dmpc molecule there is 46 atoms so in 128 it is 5888
atoms
> can u suggest me how it is helpful in making correct topology file.
As you wrote in your mail you should make two # ifdef POSRES section does it
means separatly before addind .itp file of Protein A and Protein B????????
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
>
> End of gmx-users Digest, Vol 60, Issue 116
> ******************************************
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090423/6c6827d0/attachment.html>
More information about the gromacs.org_gmx-users
mailing list