[gmx-users] Re:gmx-users Digest, Vol 67, Issue 150

[hema dhevi]

 hai justin,ya i am working on actual KALP tutorial onlyhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmxtutorials/membraneprotein/index.htmland i am using the pdb file which is given in the website. This is the first time i am doing MD simulation for transmembrane proteins before using the protein of my interest i tried it with the peptide given the tutorial.hereby i am attaching the .mdp file which i am using ; minim.mdp  used as input into grompp to generate em.tpr; Parameters describing what to do, when to stop and what to saveintegrator= steep; Algorithm (steep = steepest descent minimization)emtol= 1000.0; Stop minimization when the maximum force < 1000.0 kJ/mol/nmemstep= 0.01; Energy step sizensteps= 50000; Maximum number of (minimization) steps to perform; Parameters describing how to find the neighbors of each atom and how to calculate the interactionsnstlist= 1; Frequency to update the neighbor list and long range forcesnstype= grid; Method to determine n
 eighbor list (simple, grid)rlist= 1.2; Cutoff for making neighbor list (short range forces)coulombtype= PME; Treatment of long range electrostatic interactionsrcoulomb= 1.2; Shortrange electrostatic cutoffrvdw= 1.2; Shortrange Van der Waals cutoffpbc= xyz ; Periodic Boundary Conditions (yes/no)thank youwith regards,N.Hema Dhevi Original message From:gmxusersrequest at gromacs.org< gmxusersrequest at gromacs.org >Date: 30 Nov 09 19:38:18Subject:gmxusers Digest, Vol 67, Issue 150To: gmxusers at gromacs.orgSend gmxusers mailing list submissions to gmxusers at gromacs.orgTo subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmxusers or, via email, send a message with subject or body 'help' to gmxusersrequest at gromacs.orgYou can reach the person managing the list at gmxusersowner at gromacs.orgWhen replying, please edit your Subject line so it is more specific than "Re: Contents of gmxusers digest..." Today's Topics: 1. Re: Re: How to make carbon nan
 otube infinite? (Justin A. Lemkul)2. trjconv pbc cluster with rhombic dodecahedron box (chris.neale at utoronto.ca)3. Re: gmxusers Digest, memory allocation error (Justin A. Lemkul)4. amber force field in Gromacs (servaas)5. Survey: 3 minutes of your time (Pieter van 't Hof)6. Survey: 3 minutes of your time (Pieter van 't Hof) Message: 1 Date: Mon, 30 Nov 2009 08:05:45 0500 From: "Justin A. Lemkul"Subject: Re: [gmxusers] Re: How to make carbon nanotube infinite? To: Discussion list for GROMACS usersMessageID:ContentType: text/plain; charset=ISO88591; format=flowedCun Zhang wrote: > hi, Justin.Thank you for your meticulous and patient explanation ! >> Before I see this post, I misunderstood the meaning of sharing bonds. > I thought note only the bonds,but also the angles and the dihedrals > should be added to top file.I see now that I should have been more careful in my explanation.It is betterstated that *bonded parameters* should extend across periodic boundaries, notjust bond
 s.But the same principle applies.>> It was so complicated to deal manually that I wrote that script. > That's sensible, but I didn't understand what your scripting was doing withrenumbering and all that.Just add the appropriate parameters to the .top,given the numbering in the coordinate file.> I will read the doucment you mentioned carefully .The CNT howto was painstakingly assembled by Chris Stiles a few years ago aftermany conversations like this one.He has done a nice service by assembling thetutorial.I believe it applies to version 3.3.3, but many of the principles arethe same.Remember, as I suggested before, that x2top from the 3.3.3distribution works with the pbc option, which does all of the complicated workfor you.Not a bad option for your initial topology generation.>And I will fix these notes and warnings as grompp and mdrun suggest. > Good idea :)Justin========================================Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Bi
 ochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 2319080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin======================================== Message: 2 Date: Mon, 30 Nov 2009 08:18:42 0500 From: chris.neale at utoronto.ca Subject: [gmxusers] trjconv pbc cluster with rhombic dodecahedron box To: gmxusers at gromacs.org MessageID:ContentType: text/plain;charset=ISO88591;DelSp="Yes"; format="flowed"Hi Daniel, what Tsjerk has suggested is really the only way to go here. If your cluster is not whole in the first frame, you can do it this way:1. use trjconv pbc cluster to make your cluster whole in a frame near the start of your trajectory. If the first frame enters the infinite loop, then try the second frame, etc.2. Make a new .tpr based on this clustered .gro3. run trjconv pbc nojumpChris. original message Hi Daniel,This doesn't exactly answer your question, but if your vesicle is whole at the start, can't you better keep it that way using pbc nojump? I
 f necessary, you can also recenter afterwards.Hope it helps,TsjerkOn Mon, Nov 30, 2009 at 12:24 PM, Daniel Partonwrote:[Hide Quoted Text] Hi,I am running a coarsegrained simulation of a lipid vesicle (~70,000 particles), using a rhombic dodecahedron box to limit the amount of solvent I require.The vesicle (unsurprisingly) moves over the periodic boundaries during the simulation.Various analyses I am conducting require the vesicle to be whole, so I have been trying to use trjconv with the pbc cluster option, selecting the lipids as the group to be clustered.I am only interested in the lipid behaviour, so I am using a trajectory with only the lipids included.However, at certain frames, the program seems to enter an infinite loop, producing many lines of the following sort of information:.... COM: 12.445 5.93415.354iter = 2359 COM: 12.675 6.135 3.094iter = 2360 COM: 12.455 5.93415.368iter = 2361 COM: 12.686 6.131 3.116iter = 2362 COM: 12.454 5.94515.396iter = 2363 COM: 12.720 6
 .168 3.176iter = 2364 COM: 12.461 5.94715.435iter = 2365 COM: 12.731 6.174 3.221iter = 2366 COM: 12.468 5.94515.475iter = 2367 COM: 12.723 6.172 3.247iter = 2368 ....This is using gromacs version 3.2.1, as with any later version I have tried (3.3.3, 4.0.4, 4.0.5), trjconv pbc clustwon't work at all, even with cubic simulation boxes.I have successfully used version 3.2.1 many times for this purpose when dealing with cubic simulation boxes.I have tried many different ways to get this to work, such as converting to the compact representation before clustering.Also, the frame where the program is the first one where a lipid has moved over a periodic boundary, when the system is viewed as the compact representation.The same behaviour occurs when that frame is dumped out as a .gro file and the program is run on that file only.Does anyone have any idea how to get this to work?Any help would be much appreciated!Please let me know if you need more information about my simulation setu
 p.Daniel PartonMessage: 3 Date: Mon, 30 Nov 2009 08:38:21 0500 From: "Justin A. Lemkul"Subject: Re: [gmxusers] gmxusers Digest, memory allocation error To: "Gromacs Users' List"MessageID:ContentType: text/plain; charset=UTF8; format=flowedhema dhevi wrote: >> hi justin, >> thanks for your reply >> Totally I have 6126 atoms (residues + DPPC ) I am using the same pdb file > and lipid pdb (DPPC128) which is given in the KAPL tutorial. > OK, just to clarify  are you working on the actual KALP tutorial when thiserror comes up, or are you working on your own system?I am not 100% clear fromwhat you've described.Your previous message said you had some bacterialprotein, and now you're talking about the KALP system.Can you post the .mdp file you're using?Justin> E ven tried it without adding any solvents to it, I am getting the same> error (memory allocation). >> My system has 15.6 GB free space its a HP workstation with 2GB RAM. >> looking for ur reply at the earliest. >> Thanks in a
 dvance >> with regards, > N.Hema Dhevi >>>  Original message  > From:Justin A. Lemkul< jalemkul at vt.edu > > Date: 29 Nov 09 02:49:42 > Subject: Re: [gmxusers] gmxusers Digest, memory allocation error > To: hema dhevi , Discussion list for GROMACS users >>>> hema dhevi wrote: >> Dear all, >> >> I am doing MD simulation for a bacterial inner transmembrane protein. >> I need to know which unit of lipid molecule i should take for > building >> the lipid bilayer. >> >> I made a trial run with DPPC. I was referring KAPL tutorial for my >> simulation. I made all the alteration in the topology file and in > the >> itp file, as it is mentioned in the >> tutorial but i wouldnt run after inflategro step ie during grompp > i am >> getting memory allocation error. >> >> Hereby I am attaching the erro r msg i got from grompp >> >> >> grompp f ion.mdp c system.pdb p topolprotein.top o ions.tpr >> >> >> Program grompp, VERSION 3.3.3 >> Source code file: smalloc.c, line: 137 >> >> Fatal error
 : >> realloc for nnb>a[i][nre] (103103576 bytes, file topexcl.c, line > 101, >> nnb>a[i][nre]=0x0x33b3c3a0) >>  >> >> "Can't You Make This Thing Go Faster ?" (Black Crowes) >> >> : Cannot allocate memory >> Program grompp, VERSION 4.0.5 >> Source code file: smalloc.c , line: 179 >> >> Fatal error: >> Not enough memory. >> Failed to realloc 244312864 bytes for nnb>a[i][nre], >> nnb>a[i][nre]=0x22deb4d8 (called from file topexcl.c, line 102) >>  >>  >> >> "It's Against the Rules" (Pulp Fiction) >> : Cannot allocate memory >> >> >> I think i didnt made any error in file preparation and alteration of >> .itp and .top file. Because I tried it with 2 DPPC molecule it was >> working fine. when i am trying with the whole set of 128 molecules of >> DPPC i am facing this problem. Is this a problem something related to >> Memory of system if so what is the requirement for making this run >> possible. >> >> How many atoms are in your system? How much memory do you have > available on th
 e > machine you're using? The general solutions can be found here: >> http://www.gromacs.org/Documentation/Errors#Cannotallocatememory >> Justin >>> I got struck up in my work I am highly in need of ur help... >> >> >> Thanks in advance< /span> >> >> with regards, >> N.Hema Dhevi >> >> > ======================================== >> Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 2319080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> ======================================== > ========================================Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 2319080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin======================================== Message: 4 Date: Mon, 30 Nov 2009 14:29:56 +0100 From: servaasSubject: [gmxusers] amber force field in Groma
 cs To: "gmxusers at gromacs.org"MessageID:ContentType: text/plainHello,I tried using the amber force field in GROMACS. I proceeded as follows: Determined my parameters with RED/ANTECHAMBER/tleap converted them with amb2gmx.pl(or with acpypi, problem is the same) to gromacs coordinate and topology files. It concerns a modified nucleotide. I minimized with steepest descent, everything was fine.When I tried running a simulation in single precision with this .mdp file (only nucleotide without solvent):integrator = mddt = 0.002 nsteps = 250000 nstcomm= 1;output nstxout = 1 nstvout = 1 nstfout = 0 nstlog= 500 nstenergy = 1nstlist= 10 nstype= grid rlist= 1.2 coulombtype= PME rcoulomb = 1.2 vdwtype= cutoff rvdw = 1.2fourierspacing = 0.12 pmeorder= 4 ewaldrtol = 1e5;constraints constraints= allbonds ;temperature coupling is on Tcoupl= vrescale taut = 0.1 tcgrps = system reft = 300pcoupl= noI get LINCS errors and eventually a crash. Now I tried running the same simulation with the same f
 orce field parameters in amber and everything was fine.I also ran the calculation in GROMACS with double precision here again everything was fine... I also tried running a small nucleic acid fragment (so no modified parameters here)that I created intleap and converted to GROMACS again this crashes with lincs errors in GROMACS. When I look at the trajectories it is the O4' of the ribose who clashes with the O3'. The fact that I still get this problem with non modified amber parameters makes me thing there is something wrong with my .mdp file to run with amber FF, any suggestions?Strange also that double precision seems to work just fine....Message: 5 Date: Mon, 30 Nov 2009 14:49:12 +0100 From: Pieter van 't HofSubject: [gmxusers] Survey: 3 minutes of your time To: gmxusers at gromacs.org MessageID:ContentType: text/plainHello,My name is Pieter van 't Hof. As part of my Master thesis in computer science I am currently extending Gromacs and VMD to visualize short range Lennard Jon
 es potentials and Coulomb forces during interactive molecular dynamics simulations. In order to choose a representation method which is suitable for the most people, I designed a little survey with 7 multiple choice questions. If some of you (preferably people who use Gromacs mainly for proteinligand interactions) would fillin this survey, it is greatly appreciated.Thank you very much in advance. Sincerely,Pieter van 't Hof Utrecht University, The Netherlands Please help Logica to respect the environment by not printing this email/ Pour contribuer comme Logica au respect de l'environnement, merci de ne pas imprimer ce mail /Bitte drucken Sie diese Nachricht nicht aus und helfen Sie so Logica dabei, die Umwelt zu schützen. /Por favor ajude a Logica a respeitar o ambiente nao imprimindo este correio electronico.This email and any attachment is for authorised use by the intended recipient(s) only. It may contain proprietary material, confidential information and/or be subject 
 to legal privilege. It should not be copied, disclosed to, retained or used by, any other party. If you are not an intended recipient then please promptly delete this email and any attachment and all copies and inform the sender. Thank you. Message: 6 Date: Mon, 30 Nov 2009 14:52:21 +0100 From: Pieter van 't HofSubject: [gmxusers] Survey: 3 minutes of your time To: gmxusers at gromacs.org MessageID:ContentType: text/plainHello,My name is Pieter van 't Hof. As part of my Master thesis in computer science I am currently extending Gromacs and VMD to visualize short range Lennard Jones potentials and Coulomb forces during interactive molecular dynamics simulations. In order to choose a representation method which is suitable for the most people, I designed a little survey with 7 multiple choice questions. If some of you (preferably people who use Gromacs mainly for proteinligand interactions) would fillin this survey, it is greatly appreciated.The survey is located at http://www.th
 esistools.com/?qid=95789Thank you very much in advance. Sincerely,Pieter van 't Hof Utrecht University, The Netherlands Please help Logica to respect the environment by not printing this email/ Pour contribuer comme Logica au respect de l'environnement, merci de ne pas imprimer ce mail /Bitte drucken Sie diese Nachricht nicht aus und helfen Sie so Logica dabei, die Umwelt zu schützen. /Por favor ajude a Logica a respeitar o ambiente nao imprimindo este correio electronico.This email and any attachment is for authorised use by the intended recipient(s) only. It may contain proprietary material, confidential information and/or be subject to legal privilege. It should not be copied, disclosed to, retained or used by, any other party. If you are not an intended recipient then please promptly delete this email and any attachment and all copies and inform the sender. Thank you. gmxusers mailing list gmxusers at gromacs.org http://lists.gromacs.org/mailman/listinfo/gmxusers Please se
 arch the archive at http://www.gromacs.org/search before posting!End of gmxusers Digest, Vol 67, Issue 150 ****************************************** 
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