[gmx-users] about POPC in Gromacs
Hello all: I am a new GROMACS user. I am learning g_membrane in GROMCAS these days. It is said that the latest CHARMM36 with pre-equilibrium POPC performed very well for membrane simulation and I try to use the POPC PDB file in the website. http://terpconnect.umd.edu/~jbklauda/research/download.html However, when I try to run pdb2gmx for the POPC file in the above link with command: pdb2gmx -f popc.pdb -o popc_por.gro -water tip3p it is said: --log--- There are 0 hydrogen bonds Warning: Starting residue POPC1 in chain not identified as Protein/RNA/DNA. Warning: Starting residue POPC2 in chain not identified as Protein/RNA/DNA. Warning: Starting residue POPC3 in chain not identified as Protein/RNA/DNA. Warning: Starting residue POPC4 in chain not identified as Protein/RNA/DNA. Warning: Starting residue POPC5 in chain not identified as Protein/RNA/DNA. More than 5 unidentified residues at start of chain - disabling further warnings. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully Opening force field file /soft/gromcas-4.5.4/share/gromacs/top/charmm36.ff/aminoacids.arn --- Program pdb2gmx, VERSION 4.5.4 Source code file: pdb2gmx.c, line: 655 Fatal error: Atom H11 in residue POPC 1 was not found in rtp entry POPC with 134 atoms while sorting atoms. -log- So, I am wondering does anybody has any idea about how to solve this problem? I would be very appreciated for your such kind helps. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] My problem is How to define 5-methyl cytosine by amberff port in gromacs?
Hi all
I have inserted a new residue (DM instead of 5CM) and changed relative
files(dna.rtp,dna.r2b,dna.hdb,dna.arn ,residutypes.dat,defselection.dat),
but I have fatal erorrs in grompp:
{erorr1:[file epo0003-DNA-chain-A.itp ,line 2322]:
No default Angletypes}
{erorr2:[file epo0003-DNA-chain-A.itp ,line 3679]:
No default Improper Dih.types}
{erorr3:[file epo0003-DNA-chain-B.itp ,line 2322]:
No default Angletypes}
{erorr4:[file epo0003-DNA-chain-B.itp ,line 3679]:
No default Improper Dih.types}
anyhelp is greatly appreciate!
Best wishes
mona
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Re: [gmx-users] Plan for energy minimization, NPT equilibration, and NPT dynamics
Hi Andrew, looking at your protocol, perhaps I can help thermo- and barostating. This are very important issues as they decide if your final trajectory samples a canonical phase space that should correspond to the desired ensemble( Tuckerman and Martyna, J. Phys. Chem. B 2000, 104, 159-178, DOI:10.1021/jp992433y is a very good review for this topic ). You are using Nose-Hoover(NH) for both, equilibration and production. However to drive a system into equilibrium you should perhaps switch to the v-rescale thermostat. It is more stable and samples the phase canonically as well as NH. The shorter you make the coupling time, the faster you reach equilibrium, but the stronger you disturb the correlations in the system. For the production run the NC scheme allows to control the time scales were correlations are affected with the coupling parameter tau_t, while for v-rescale tau_t is just a measure how strong the thermostat is coupled to the system. As you want to simulate a canoncial NPT ensemble, the only possibility for pressure coupling is parrinello-rahman or mttk, while the latter one is just an extension of the first one. However to equilibrate the system berendsen should be the method of choice, though it does not sample canonically. The rules for the coupling parameter are similar as in the case of temperature coupling. For mttk and pr, tau_p is a measure for the time scale where correlations are conserved, while for berendsen tau_p measures the strength of the coupling. For the pressure coupling, short coupling times introduce very large fluctuations of the box size, so that it can take also a very long time to reach equilibrium. Hope this helps a little bit. /Flo On Sat, 2011-05-28 at 21:40 -0400, Andrew DeYoung wrote: Hi, In the past few weeks, I have run some simulations of 254 water molecules. Although I got some results, I did not do things in the best way. For example, I threw away my equilibrated ensemble before doing my production run, as was kindly pointed out to me on this mailing list last week. In trying to think more carefully about the input parameters and the commands I use, I have done some more reading, particularly in the very helpful lysozyme tutorial (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lyso zyme/index.html) by Justin Lemkul. In planning another simulation, I would like to understand better reasonable parameters to use and the correct commands to use. If you have time, can you please look at the pdf file at http://www.andrew.cmu.edu/user/adeyoung/may28.pdf that I have created? If you have time, I have some questions about it. On page 1, I have typed some possible parameter files (adapted from Justin Lemkul's lysozyme tutorial); on page 2, I have typed a list of commands (also adapted from the lysozyme tutorial) I may use in my run. I plan to do energy minimization, NPT equilibration, and NPT MD (for NPT, I plan to use Berendsen pressure coupling and Nose-Hoover temperature coupling) using Gromacs 4.5.4. If you have time, here are my questions about the pdf file: --- (i) In equilibration, what is a reasonable value of nstlist to use? The Gromacs manual on page 18 says that nstlist is typically 10, but is it true that, in principle, the smaller that nstlist is (that is, the more often the pairlist is updated), the more accurate the simulation is, at greater computational cost? As a rule of thumb, should I use nstlist = 10 or something smaller? I have access to a cluster, so I don't have too many worries about computational cost, to a reasonable extent. (ii) In equilibration, what is a reasonable value of the time constant tau_p to use for Berendsen pressure coupling? The default is 1 ps, although I have seen tutorials where people use tau_p as high as 2 ps or as low as 0.1 ps. The Gromacs manual on page 32 gives a relationship for the change in pressure with respect to time for Berendsen pressure coupling: dP/dt = (P_0 - P)/tau_p where P_0 is the reference pressure (ref_p in Gromacs). So it seems that the smaller the tau_p, the faster the pressure relaxes toward the reference pressure. So, naively, it would be best to use a small tau_p. However, am I correct in thinking that, on the other hand, if I make tau_p too small for a fixed step size dt, significant inaccuracies may result? (iii) In equilibration, is it reasonable to set DispCorr = no? I won't be using my equilibration results for any detailed analysis; I only wish to generate a (hopefully) reasonable ensemble and relax the pressure to the reference pressure. (iv) Similarly, in production, is it reasonable to set DispCorr = no? I suppose that it depends on what one ultimately wants to calculate using the final MD production results. Since I am still at the stage of getting familiar with Gromacs, I will be doing only simple analyses (RDF, MSD, velocity autocorrelation function, and
Re: [gmx-users] My problem is How to define 5-methyl cytosine by amberff port in gromacs?
On 29/05/2011 7:29 PM, Masomeh Dehghani wrote:
Hi all
I have inserted a new residue (DM instead of 5CM) and changed relative
files(dna.rtp,dna.r2b,dna.hdb,dna.arn ,residutypes.dat,defselection.dat),
but I have fatal erorrs in grompp:
{erorr1:[file epo0003-DNA-chain-A.itp ,line 2322]:
No default Angletypes}
{erorr2:[file epo0003-DNA-chain-A.itp ,line 3679]:
No default Improper Dih.types}
{erorr3:[file epo0003-DNA-chain-B.itp ,line 2322]:
No default Angletypes}
{erorr4:[file epo0003-DNA-chain-B.itp ,line 3679]:
No default Improper Dih.types}//
anyhelp is greatly appreciate!//
As I said last time, you need to look at those lines in your molecule
.itp file and see why they don't match the type definitions in your
forcefield .itp files.
Mark
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Re: [gmx-users] Minimum periodic distance
Hi Kavya, shortest periodic distance is 1.39714 (nm) at time 21824 (ps), between atoms 2062 and 3688 where 2062 is a protein atom and 21824 is a water molecule. 21824 is the time in ps at which the two atoms indicated, 2062 and 3688, are at the short distance given. You can dump the frame with trjconv and have a look. Probably your molecule stretched, or you solvated in a rectangular box and the protein rotated. In the first case, set a larger distance, in the second, use a rhombic dodecahedron. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] hi
Hi all.. I want to ask if it is possible to restart the md run if due to power problem final md run not completed means initiating md from where is stop due to any reason? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] hi
On 29 May 2011 14:45, rashi.pari...@gmail.com wrote: Hi all.. I want to ask if it is possible to restart the md run if due to power problem final md run not completed means initiating md from where is stop due to any reason? You can supply the checkpoint file written out, by -cpi option to mdrun and continue your simulation. For more information see mdrun -h. Best Wishes, Sarath -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Re: [gmx-users] hi
thanx sarath 4r reply..can u expalin little bit more..I did not get from mdrun -h. On , Sarath Chandra Dantu dsar...@gwdg.de wrote: On 29 May 2011 14:45, rashi.pari...@gmail.com wrote: Hi all.. I want to ask if it is possible to restart the md run if due to power problem final md run not completed means initiating md from where is stop due to any reason? You can supply the checkpoint file written out, by -cpi option to mdrun and continue your simulation. For more information mdrun -h. Best Wishes, Sarath -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] hi
On 29/05/2011 10:45 PM, rashi.pari...@gmail.com wrote: Hi all.. I want to ask if it is possible to restart the md run if due to power problem final md run not completed means initiating md from where is stop due to any reason? Please use a meaningful subject line in emails. See http://www.gromacs.org/Documentation/How-tos/Doing_Restarts Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] hi
On May 29, 2011, at 20:45, rashi.pari...@gmail.com wrote: Hi all.. I want to ask if it is possible to restart the md run if due to power problem final md run not completed means initiating md from where is stop due to any reason? Suppose your .tpr is topol.tpr mdrun -cpi state.cpt Or suppose your .tpr is my.tpr You may try mdrun -deffnm my -cpi my.cpt As suggested by others. Start learning read mdrun --h -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] protein-ligand interaction
Dear Justin, I used -res flag with the following command but I get pairs of values in the output files. is there any mistake related with the command I used? g_rmsf -s run.tpr -f run.xtc -o rmsf.xvg -od rmsdev.xvg -res 2011/5/29 jalem...@vt.edu Quoting ahmet y?ld?r?m ahmedo...@gmail.com: Dear Justin, You said You can get a per-residue RMSD by using g_rmsf -od to see the effect of the ligand on each residue. 1. Can you explain the difference between what goes into the -o file, and what goes into the -od file? The -o output is RMSF; the -od output is RMSD. 2. How should I create a index file to see the effect of the ligand on each residue? Do I have to create the index file? g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg Is this command sufficient to see the effect of the ligand on each residue? An index file should not be necessary. By default, the output is per atom, so use the -res flag if you want the measurements averaged over all atoms in each residue. The command is sufficient to measure the RMSD per residue. Whether or not that is sufficient is up to you. 3. Furthermore, can you suggest the other analysis tools to see the effect of the ligand *on protein*? You should identify the quantities you wish to measure, then read in the Gromacs manual about the different utility programs available. You'll learn far more that way. -Justin Thanks in advance 2011/5/28 jalem...@vt.edu Quoting ahmet y?ld?r?m ahmedo...@gmail.com: Dear users, I want to investigate *Ligand effect *on the protein . To investigation the interaction of protein-ligand: *RMSD calculations:* 1. a) RMSD of Backbone b) RMSD of Backbone+ligand 2. a) RMSD of Protein b) RMSD of Protein+ligand 3. a) RMSD of Protein-H b) RMSD of Protein-H+ligand Which one would you recommend ( 1., 2., and 2.choice)? Unless the effect of your ligand is very large (i.e., the whole protein is significantly more or less stable in the presence of the ligand), then likely none of these analyses will be particularly illustrative as they are not very sensitive to small changes. You can get a per-residue RMSD by using g_rmsf -od to see the effect of the ligand on each residue. Otherwise, the most common quantity measured is backbone RMSD. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet YILDIRIM -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Restarting replica exchange simulation
Hi, I was running a replica exchange simulation in a PBS queue which was killed as my simulation crossed the maximum time limit. I was planning to restart the simulation. I am using gromacs 4.0.7 I was wondering what should be the command line arguement for the multiple .cpt file for restarting the replica exchange simulation. My .cpt files are named like state0.cpt,state1.cpt,state2.cpt etc while my .tpr file topol_0.tpr,topol_1.tpr etc. Should I put state*.cpt for mentioning the multiple .cpt files ? i.e Will it be something like : mpirun -np $NPROCS ~/UTIL_icc/gromacs-4.0.7/bin/mdrun_4mpi -cpi state*.cpt -s topol_.tpr -v -multi 40 -replex 1000 log_replex_test Thanks Sanku-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] where can I download POPC membrane file?
Dear all: I would like to use charmm36 and POPC for membrane protein simulation. and I am wondering where can I download charmm36 pre-pribriumed POPC PDB and topol file for gromacs? Thank you very much Best -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] where can I download POPC membrane file?
You can build it using VMD (VIsual Molecular Dynamics) 2011/5/30 albert leu...@yeah.net Dear all: I would like to use charmm36 and POPC for membrane protein simulation. and I am wondering where can I download charmm36 pre-pribriumed POPC PDB and topol file for gromacs? Thank you very much Best -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re:Re: [gmx-users] where can I download POPC membrane file?
But I don't think it is pre-equilibrium POPC membrane.. and more over, the position from VMD is not pre-aligned with OPM database. It would be a great problem for putting our protein in the membrane.. At 2011-05-30，Sergio Manzetti sergio.manze...@vestforsk.no wrote: You can build it using VMD (VIsual Molecular Dynamics) 2011/5/30 albertleu...@yeah.net Dear all: I would like to use charmm36 and POPC for membrane protein simulation. and I am wondering where can I download charmm36 pre-pribriumed POPC PDB and topol file for gromacs? Thank you very much Best -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive athttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it togmx-users-requ...@gromacs.org. Can't post? Readhttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] is it possible to convert NAMD psf file to gromacas format?
Hello: I am wondering, is it possible to convert NAMD topol psf file into Gromacs topol format? Thank you very much -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] is it possible to convert NAMD psf file to gromacas format?
Il 29/05/2011 21:58, albert ha scritto: Hello: I am wondering, is it possible to convert NAMD topol psf file into Gromacs topol format? Thank you very much Hi albert, you can try with the following commands: vmd .psf .pdb topo writegmxtop output.top I recently tried with vmd1.9 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] protein-ligand interaction
Dear users, I am getting pairs of values in the output files as I said before. What is this mean? Furthermore, though my system have 451 residue, it seems as 230 residue ( and 1th residue does not seem in the out files). What could be the problem? * output file:* # This file was created Sun May 29 22:33:05 2011 # by the following command: # g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg -o rmsf.xvg -res # # g_rmsf is part of G R O M A C S: # # GROwing Monsters And Cloning Shrimps # @title RMS fluctuation @xaxis label Residue @yaxis label (nm) @TYPE xy 2 0.1217 3 0.0952 4 0.0760 5 0.0740 6 0.0613 7 0.0565 . 227 0.0785 228 0.0955 229 0.1254 230 0.1352 2 0.1181 3 0.0851 4 0.0713 5 0.0674 6 0.0645 7 0.0631 8 0.0707 9 0.0699 228 0.1034 229 0.1161 230 0.1206 29 Mayıs 2011 19:28 tarihinde ahmet yıldırım ahmedo...@gmail.com yazdı: Dear Justin, I used -res flag with the following command but I get pairs of values in the output files. is there any mistake related with the command I used? g_rmsf -s run.tpr -f run.xtc -o rmsf.xvg -od rmsdev.xvg -res 2011/5/29 jalem...@vt.edu Quoting ahmet y?ld?r?m ahmedo...@gmail.com: Dear Justin, You said You can get a per-residue RMSD by using g_rmsf -od to see the effect of the ligand on each residue. 1. Can you explain the difference between what goes into the -o file, and what goes into the -od file? The -o output is RMSF; the -od output is RMSD. 2. How should I create a index file to see the effect of the ligand on each residue? Do I have to create the index file? g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg Is this command sufficient to see the effect of the ligand on each residue? An index file should not be necessary. By default, the output is per atom, so use the -res flag if you want the measurements averaged over all atoms in each residue. The command is sufficient to measure the RMSD per residue. Whether or not that is sufficient is up to you. 3. Furthermore, can you suggest the other analysis tools to see the effect of the ligand *on protein*? You should identify the quantities you wish to measure, then read in the Gromacs manual about the different utility programs available. You'll learn far more that way. -Justin Thanks in advance 2011/5/28 jalem...@vt.edu Quoting ahmet y?ld?r?m ahmedo...@gmail.com: Dear users, I want to investigate *Ligand effect *on the protein . To investigation the interaction of protein-ligand: *RMSD calculations:* 1. a) RMSD of Backbone b) RMSD of Backbone+ligand 2. a) RMSD of Protein b) RMSD of Protein+ligand 3. a) RMSD of Protein-H b) RMSD of Protein-H+ligand Which one would you recommend ( 1., 2., and 2.choice)? Unless the effect of your ligand is very large (i.e., the whole protein is significantly more or less stable in the presence of the ligand), then likely none of these analyses will be particularly illustrative as they are not very sensitive to small changes. You can get a per-residue RMSD by using g_rmsf -od to see the effect of the ligand on each residue. Otherwise, the most common quantity measured is backbone RMSD. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet YILDIRIM -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet YILDIRIM -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before
Re:Re: [gmx-users] is it possible to convert NAMD psf file to gromacas format?
Thank you very much for kind advices. Here is some warning, and I don't know whether there would be some problem or not: ; 'fake' gromacs topology generated from topotools. ; WARNING| the purpose of this topology is to allow using the |WARNING ; WARNING| analysis tools from gromacs for non gromacs data. |WARNING ; WARNING| it cannot be used for a simulation. |WARNING At 2011-05-30，Francesco Oteri francesco.ot...@gmail.com wrote: Il 29/05/2011 21:58, albert ha scritto: Hello: I am wondering, is it possible to convert NAMD topol psf file into Gromacs topol format? Thank you very much Hi albert, you can try with the following commands: vmd .psf .pdb topo writegmxtop output.top I recently tried with vmd1.9 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] is it possible to convert NAMD psf file to gromacas format?
Topology file is suitable for analysis. I succesfully used the .top to analyse hydrogen bond and salt-bridges. I don't know if problems would arise for simulation. Il 29/05/2011 22:10, albert ha scritto: Thank you very much for kind advices. Here is some warning, and I don't know whether there would be some problem or not: ; 'fake' gromacs topology generated from topotools. ; WARNING| the purpose of this topology is to allow using the |WARNING ; WARNING| analysis tools from gromacs for non gromacs data. |WARNING ; WARNING| it cannot be used for a simulation. |WARNING At 2011-05-30??Francesco Oterifrancesco.ot...@gmail.com wrote: Il 29/05/2011 21:58, albert ha scritto: Hello: I am wondering, is it possible to convert NAMD topol psf file into Gromacs topol format? Thank you very much Hi albert, you can try with the following commands: vmd .psf .pdb topo writegmxtop output.top I recently tried with vmd1.9 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re:Re: [gmx-users] is it possible to convert NAMD psf file to gromacas format?
Thank you very much for kind messages. I am trying to convert a membrane system psf file for gromcas MD simulation. For I would like to use CHARMM36 for my POPC system, but I cannot find pre-equilibrium CAHRMM36 based POPC system. However, there is some for NAMD and I download the pdf and psf file hoping that it could be converted to related gromacs format. Do you have any idea about this? THX At 2011-05-30，Francesco Oteri francesco.ot...@gmail.com wrote: Topology file is suitable for analysis. I succesfully used the .top to analyse hydrogen bond and salt-bridges. I don't know if problems would arise for simulation. Il 29/05/2011 22:10, albert ha scritto: Thank you very much for kind advices. Here is some warning, and I don't know whether there would be some problem or not: ; 'fake' gromacs topology generated from topotools. ; WARNING| the purpose of this topology is to allow using the |WARNING ; WARNING| analysis tools from gromacs for non gromacs data. |WARNING ; WARNING| it cannot be used for a simulation. |WARNING At 2011-05-30，Francesco Oterifrancesco.ot...@gmail.com wrote: Il 29/05/2011 21:58, albert ha scritto: Hello: I am wondering, is it possible to convert NAMD topol psf file into Gromacs topol format? Thank you very much Hi albert, you can try with the following commands: vmd .psf .pdb topo writegmxtop output.top I recently tried with vmd1.9 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] is it possible to convert NAMD psf file to gromacas format?
You can solve the problem without converting from namd to gromacs. You can use the pdb you've already found to obtain a valid gromacs topology through pdb2gmx Il 29/05/2011 22:24, albert ha scritto: Thank you very much for kind messages. I am trying to convert a membrane system psf file for gromcas MD simulation. For I would like to use CHARMM36 for my POPC system, but I cannot find pre-equilibrium CAHRMM36 based POPC system. However, there is some for NAMD and I download the pdf and psf file hoping that it could be converted to related gromacs format. Do you have any idea about this? THX At 2011-05-30??Francesco Oterifrancesco.ot...@gmail.com wrote: Topology file is suitable for analysis. I succesfully used the .top to analyse hydrogen bond and salt-bridges. I don't know if problems would arise for simulation. Il 29/05/2011 22:10, albert ha scritto: Thank you very much for kind advices. Here is some warning, and I don't know whether there would be some problem or not: ; 'fake' gromacs topology generated from topotools. ; WARNING| the purpose of this topology is to allow using the |WARNING ; WARNING| analysis tools from gromacs for non gromacs data. |WARNING ; WARNING| it cannot be used for a simulation. |WARNING At 2011-05-30??Francesco Oterifrancesco.ot...@gmail.com wrote: Il 29/05/2011 21:58, albert ha scritto: Hello: I am wondering, is it possible to convert NAMD topol psf file into Gromacs topol format? Thank you very much Hi albert, you can try with the following commands: vmd .psf .pdb topo writegmxtop output.top I recently tried with vmd1.9 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re:Re: [gmx-users] is it possible to convert NAMD psf file to gromacas format?
Well, I also try to do this. But it seem that the atom name in my POPC pdb file (which I download from here http://terpconnect.umd.edu/~jbklauda/research/download.html ) is different from the the one in Gromacs topol database. There are 72 lips in the system in all. So, it would be very difficult to modify them one by one. Thank you very much At 2011-05-30，Francesco Oteri francesco.ot...@gmail.com wrote: You can solve the problem without converting from namd to gromacs. You can use the pdb you've already found to obtain a valid gromacs topology through pdb2gmx Il 29/05/2011 22:24, albert ha scritto: Thank you very much for kind messages. I am trying to convert a membrane system psf file for gromcas MD simulation. For I would like to use CHARMM36 for my POPC system, but I cannot find pre-equilibrium CAHRMM36 based POPC system. However, there is some for NAMD and I download the pdf and psf file hoping that it could be converted to related gromacs format. Do you have any idea about this? THX At 2011-05-30，Francesco Oterifrancesco.ot...@gmail.com wrote: Topology file is suitable for analysis. I succesfully used the .top to analyse hydrogen bond and salt-bridges. I don't know if problems would arise for simulation. Il 29/05/2011 22:10, albert ha scritto: Thank you very much for kind advices. Here is some warning, and I don't know whether there would be some problem or not: ; 'fake' gromacs topology generated from topotools. ; WARNING| the purpose of this topology is to allow using the |WARNING ; WARNING| analysis tools from gromacs for non gromacs data. |WARNING ; WARNING| it cannot be used for a simulation. |WARNING At 2011-05-30，Francesco Oterifrancesco.ot...@gmail.com wrote: Il 29/05/2011 21:58, albert ha scritto: Hello: I am wondering, is it possible to convert NAMD topol psf file into Gromacs topol format? Thank you very much Hi albert, you can try with the following commands: vmd .psf .pdb topo writegmxtop output.top I recently tried with vmd1.9 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] is it possible to convert NAMD psf file to gromacas format?
I guess it is tedious but, in my opinion it is more correct changing the atom name in the pdb and using gromacs topology generation tools. So you are sure the topology will be suitable for gromacs simulation. You rename atom, using the command sed. In particular: sed s/old/new/g file replaces each occurence of old with new. Once you find the correspondenze between gromacs and pdb atom name, you can solve the problem. Alternatively,you can replace atom name using some text file editor. Il 29/05/2011 22:35, albert ha scritto: Well, I also try to do this. But it seem that the atom name in my POPC pdb file (which I download from here http://terpconnect.umd.edu/~jbklauda/research/download.html ) is different from the the one in Gromacs topol database. There are 72 lips in the system in all. So, it would be very difficult to modify them one by one. Thank you very much At 2011-05-30??Francesco Oterifrancesco.ot...@gmail.com wrote: You can solve the problem without converting from namd to gromacs. You can use the pdb you've already found to obtain a valid gromacs topology through pdb2gmx Il 29/05/2011 22:24, albert ha scritto: Thank you very much for kind messages. I am trying to convert a membrane system psf file for gromcas MD simulation. For I would like to use CHARMM36 for my POPC system, but I cannot find pre-equilibrium CAHRMM36 based POPC system. However, there is some for NAMD and I download the pdf and psf file hoping that it could be converted to related gromacs format. Do you have any idea about this? THX At 2011-05-30??Francesco Oterifrancesco.ot...@gmail.com wrote: Topology file is suitable for analysis. I succesfully used the .top to analyse hydrogen bond and salt-bridges. I don't know if problems would arise for simulation. Il 29/05/2011 22:10, albert ha scritto: Thank you very much for kind advices. Here is some warning, and I don't know whether there would be some problem or not: ; 'fake' gromacs topology generated from topotools. ; WARNING| the purpose of this topology is to allow using the |WARNING ; WARNING| analysis tools from gromacs for non gromacs data. |WARNING ; WARNING| it cannot be used for a simulation. |WARNING At 2011-05-30??Francesco Oterifrancesco.ot...@gmail.comwrote: Il 29/05/2011 21:58, albert ha scritto: Hello: I am wondering, is it possible to convert NAMD topol psf file into Gromacs topol format? Thank you very much Hi albert, you can try with the following commands: vmd .psf .pdb topo writegmxtop output.top I recently tried with vmd1.9 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] GTG to GAG with amber FF99SB force field
Dear Gromacs users: I use gromacs.4-5-3 to calculate the free energy changes for the GTG to GAG alchemy process, where charge annihilation is performed first followed by soft core VDW calculation. When doing the soft core VDW calculation, I see this error message ?Fatal error: [ file gtg_vdw.top, line 314 ]: Proper Dih. multiplicity can not be perturbed 1.00!=3.00?.Line 314 has the following content ?17161824 9?The atoms with VDW radius and well depth changes include 20 CT 3THRCG2 20 -0. 12.01 CTD 0.0 12.01 ; qtot 0.0439 21 HC 3 THR HG21 21 0. 1.008 HCD 0.0 1.008; qtot 0.1081 22 HC 3THR HG22 22 0. 1.008 HCD 0.0 1.008; qtot 0.1723 23 HC 3THR HG23 23 0. 1.008 HCD 0.0 1.008; qtot 0.2365 24 OH 3THROG1 24-0. 16 OHD 0.0 16 ; qtot -0.4396 25 HO 3THRHG1 25 0. 1.008 HOD 0.0 1.008; qtot -0.0294Atom types CTD, HCD, OHD, HOD are defined in a separate file and included in the topology file. My question is how to solve this problem and a related question is whether the overall setup is correct.Best, Lishan-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How to simulate spc216.pdb in different water potentials
Dear Sir/ Madam, I would like to run simulation for water in different water potentials like spc spc/e tip3p tip4p ... But when I do pdb2gmx and genbox to solvate the box (l= 1.862) I am not able generate box of 216 molecules. Please find me a solution. Thank you in advance *With Regards,** * * * *Ravi Kumar Venkatraman,* *c/o Prof. Siva Umapathy,** * *IPC Dept., IISc.,* *Bangalore, INDIA.* *Phone No: +91-9686933963* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to simulate spc216.pdb in different water potentials
Ravi Kumar Venkatraman wrote: Dear Sir/ Madam, I would like to run simulation for water in different water potentials like spc spc/e tip3p tip4p ... But when I do pdb2gmx and genbox to solvate the box (l= 1.862) I am not able generate box of 216 molecules. Please find me a solution. You don't need pdb2gmx. All the coordinate and topology files are already provided in $GMXLIB or the force field subdirectories. Write the system .top with a text editor, generically: #include forcefield.itp #include water.itp [ system ] water [ molecules ] SOL 216 -Justin Thank you in advance *With Regards,** * * * *Ravi Kumar Venkatraman,* *c/o Prof. Siva Umapathy,** * *IPC Dept., IISc.,* *Bangalore, INDIA.* *Phone No: +91-9686933963* -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Minimum periodic distance
Hello sir, I had used a dodecahedron cell for simulation. I have run the simulation for 100ns, did you man I have to restart the simulation again? Thanking you Kavya On Sun, May 29, 2011 at 5:40 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Kavya, shortest periodic distance is 1.39714 (nm) at time 21824 (ps), between atoms 2062 and 3688 where 2062 is a protein atom and 21824 is a water molecule. 21824 is the time in ps at which the two atoms indicated, 2062 and 3688, are at the short distance given. You can dump the frame with trjconv and have a look. Probably your molecule stretched, or you solvated in a rectangular box and the protein rotated. In the first case, set a larger distance, in the second, use a rhombic dodecahedron. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Minimum periodic distance
Hello Sir, I saw the 21824th frame, it dint look unusually stretched when I superposed against the initial pdb file. there atoms were hydrogen atoms of two lysine residues.. And in the entire strttch of 100ns simulation this is the only periodic image interaction observed, Is it possible to correct it now. or should I have to redo the simulation again?? Kindly reply.. Thank you With regards M. Kavyashree On Sun, May 29, 2011 at 5:40 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Kavya, shortest periodic distance is 1.39714 (nm) at time 21824 (ps), between atoms 2062 and 3688 where 2062 is a protein atom and 21824 is a water molecule. 21824 is the time in ps at which the two atoms indicated, 2062 and 3688, are at the short distance given. You can dump the frame with trjconv and have a look. Probably your molecule stretched, or you solvated in a rectangular box and the protein rotated. In the first case, set a larger distance, in the second, use a rhombic dodecahedron. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
