[gmx-users] g_nmtraj -temp
Dear gromacs users, g_nmtraj states that to make the motion clearly visible in PyMol you might want to amplify it by setting an unrealistically high temperature. What temperature values do you usually need to use? To see nice domain movements, I need to set the temperature in the range 10-50K. Are those unrealistic temperatures “normal”? Many thanks, Rui Rodrigues -- 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] eigenvectors with nan values
Hi Mark, Thanks for replying. De: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] Em Nome De Mark Abraham [mark.abra...@anu.edu.au] Enviado: segunda-feira, 20 de Agosto de 2012 0:23 Para: Discussion list for GROMACS users Assunto: Re: [gmx-users] eigenvectors with nan values On 20/08/2012 4:34 AM, Joaquim Rui de Castro Rodrigues wrote: Dear Gromacs users, I'm having problems with g_covar because sometimes it produces eigenvectors with nan values. This is related with a previous post (http://lists.gromacs.org/pipermail/gmx-users/2012-July/073492.html). I checked the integrity of my xtc and tpr/pdb input files, and everything seems fine, as the following works OK: echo System System | /usr/local/gromacs455/bin/g_covar455 -s mainchain_init.tpr -f mainchain_apo.xtc -o eigenvalues.xvg -v eigenvectors.trr -xpma covara.xpm -xpm covar.xpm -l covar.log but running g_covar with parts of the same trajectory gives eigenvectors with nan values: echo System System | /usr/local/gromacs455/bin/g_covar455 -s mainchain_init.tpr -f mainchain_apo.xtc -b 2000 -e 22000 -o eigenvalues_1.xvg -v eigenvectors_1.trr -xpma covara_1.xpm -xpm covar_1.xpm -l covar_1.log -av av_1.pdb -ascii covar_1.dat echo System System | /usr/local/gromacs455/bin/g_covar455 -s mainchain_init.tpr -f mainchain_apo.xtc -b 22000 -e 42000 -o eigenvalues_2.xvg -v eigenvectors_2.trr -xpma covara_2.xpm -xpm covar_2.xpm -l covar_2.log -av av_2.pdb -ascii covar_2.dat eigenvectors_1.trr has one frame with all coordinates set to nan; eigenvectors_2.trr has 17. I don't see anything obviously wrong with the other files produced (xvg, xpm, pdb). What could be the problem? Not sure. Does the number of frames reported read by g_covar make sense? What's the frame frequency in your .xtc? What happens if you use trjconv to make the trajectory subsets before using g_covar without -b and -e? What's in System? Does double precision behave the same? Are the corresponding eigenvalues also nan? Mark The number of frames read by g_covar are the expected ones: whole: Read 4 frames from mainchain_apo.xtc (time 2000 to 41999 ps) part1: Read 2 frames from mainchain_apo.xtc (time 2000 to 21999 ps) part2: Read 2 frames from mainchain_apo.xtc (time 22000 to 41999 ps) The timestep of the xtc is 1 ps. I created two trajectory subsets: trjconv -f mainchain_apo.xtc -b 2000 -e 22000 -o mainchain_apo_part1.xtc trjconv -f mainchain_apo.xtc -b 22000 -e 42000 -o mainchain_apo_part2.xtc and run g_covar without -b and -e, and I get identical eigenvectors (as well as identical averaged pdb and xpm matrices). System contains 4600 mainchain protein atoms: Group 0 ( System) has 4600 elements Group 1 (Protein) has 4600 elements Group 2 ( Protein-H) has 4600 elements Group 3 (C-alpha) has 1150 elements Group 4 ( Backbone) has 3450 elements Group 5 ( MainChain) has 4600 elements Group 6 ( MainChain+Cb) has 4600 elements Group 7 (MainChain+H) has 4600 elements Group 8 ( SideChain) has 0 elements Group 9 (SideChain-H) has 0 elements The mainchain atoms in the xtc were extracted with trjconv; the tpr containing only mainchain atoms was obtained with tpbconv. The corresponding eigenvalues are numbers and are equal to the timestep found in the eigenvectors.trr trajectories, as it should be. I've just finished to run in double precision, and the nan values are all gone. That solved the problem :-) Still, I wonder what went wrong with single precision. Many thanks, Rui Rodrigues -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] eigenvectors with nan values
Dear Gromacs users, I'm having problems with g_covar because sometimes it produces eigenvectors with nan values. This is related with a previous post (http://lists.gromacs.org/pipermail/gmx-users/2012-July/073492.html). I checked the integrity of my xtc and tpr/pdb input files, and everything seems fine, as the following works OK: echo System System | /usr/local/gromacs455/bin/g_covar455 -s mainchain_init.tpr -f mainchain_apo.xtc -o eigenvalues.xvg -v eigenvectors.trr -xpma covara.xpm -xpm covar.xpm -l covar.log but running g_covar with parts of the same trajectory gives eigenvectors with nan values: echo System System | /usr/local/gromacs455/bin/g_covar455 -s mainchain_init.tpr -f mainchain_apo.xtc -b 2000 -e 22000 -o eigenvalues_1.xvg -v eigenvectors_1.trr -xpma covara_1.xpm -xpm covar_1.xpm -l covar_1.log -av av_1.pdb -ascii covar_1.dat echo System System | /usr/local/gromacs455/bin/g_covar455 -s mainchain_init.tpr -f mainchain_apo.xtc -b 22000 -e 42000 -o eigenvalues_2.xvg -v eigenvectors_2.trr -xpma covara_2.xpm -xpm covar_2.xpm -l covar_2.log -av av_2.pdb -ascii covar_2.dat eigenvectors_1.trr has one frame with all coordinates set to nan; eigenvectors_2.trr has 17. I don't see anything obviously wrong with the other files produced (xvg, xpm, pdb). What could be the problem? Thanks for your time, Rui Rodrigues-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] 2 chain protein and VMD
Hi, You could do something like this: set sel1 [atomselect top residue 0 to 499] $sel1 set chain A set sel2 [atomselect top residue 500 to 999] $sel2 set chain B Hope this helps, Rui Rodrigues De: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] Em Nome De Acoot Brett [acootbr...@yahoo.com] Enviado: sábado, 18 de Agosto de 2012 9:35 Para: Discussion list for GROMACS users Assunto: [gmx-users] 2 chain protein and VMD Dear All, After the production MD for a 2-chain protein complex (chain A and chain B) was done, I used VMD to observe the trajectory. I want to color the 2 chains in different color. However it seems during the observation of the trajectory by VMD, VMD treated both of the 2 chains as chain X, and thus the 2 chains cannot be colored differently. Do you have any method or suggestion to color the 2 chains in different color by VMD in the trajectory observation process? Cheers, Acoot -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] nan in g_anaeig -over
Mark,
You are right. I've run gmxdump on the eigenvectors and I can see nan
coordinates in 3 consecutive frames (13589 to 13591):
eigenvectors.trr frame 13589:
natoms= 4600 step= 13588 time=-3.2829557e-06 lambda= 0
box (3x3):
box[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
box[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
box[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
x (4600x3):
x[0]={ nan, nan, nan}
x[1]={ nan, nan, nan}
x[2]={ nan, nan, nan}
x[3]={ nan, nan, nan}
x[4]={ nan, nan, nan}
x[5]={ nan, nan, nan}
I've just re-run g_covar the the same input and i got identical eigenvectors
(checked with gmxcheck and diff). I'll have to check my input to g_covar...
Thanks,
Rui Rodrigues
De: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] Em Nome De
Mark Abraham [mark.abra...@anu.edu.au]
Enviado: quinta-feira, 26 de Julho de 2012 16:48
Para: Discussion list for GROMACS users
Assunto: Re: [gmx-users] nan in g_anaeig -over
On 27/07/2012 12:31 AM, Joaquim Rui de Castro Rodrigues wrote:
Dear all,
I am getting a nan while calculating the overlap between covariance matrices
(in this case, using the same vectors for -v and -v2):
g_anaeig455 -v atp/eigenvectors.trr -v2 atp/eigenvectors.trr -over
overlap_atp-atp
I tried different gromacs versions, different -last values, and also setting
the -eig and -eig2 flags, with the same results.
Any idea what could be wrong here?
Please find below the content of the .xvg file and the ouput from g_anaeig.
Thanks for your time,
Rui Rodrigues
Here is the content of overlap_atp-atp.xvg:
(...)
Here is the complete ouput from g_anaeig:
(...)
Something's wrong with your eigenvectors. Look at the other output files
and/or gmxdump the eigenvector files.
Mark
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[gmx-users] nan in g_anaeig -over
Dear all, I am getting a nan while calculating the overlap between covariance matrices (in this case, using the same vectors for -v and -v2): g_anaeig455 -v atp/eigenvectors.trr -v2 atp/eigenvectors.trr -over overlap_atp-atp I tried different gromacs versions, different -last values, and also setting the -eig and -eig2 flags, with the same results. Any idea what could be wrong here? Please find below the content of the .xvg file and the ouput from g_anaeig. Thanks for your time, Rui Rodrigues Here is the content of overlap_atp-atp.xvg: @title Subspace overlap @xaxis label Eigenvectors of trajectory 2 @yaxis label Overlap @TYPE xy @ subtitle using 8 eigenvectors of trajectory 1 1 0.125 2 0.250 3 0.375 4 0.500 5 0.625 6 0.750 7 0.875 8 1.000 9 1.000 10 1.000 (...) 13586 1.000 13587 1.000 13588nan 13589nan 13590nan (...) 13799nan 13800nan Here is the complete ouput from g_anaeig: :-) G R O M A C S (-: S C A M O R G :-) VERSION 4.5.5 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. 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. :-) /usr/local/gromacs455/bin/g_anaeig455 (-: Option Filename Type Description -v atp/eigenvectors.trr InputFull precision trajectory: trr trj cpt -v2 atp/eigenvectors.trr Input, Opt! Full precision trajectory: trr trj cpt -f traj.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -s topol.tpr Input, Opt. Structure+mass(db): tpr tpb tpa gro g96 pdb -n index.ndx Input, Opt. Index file -eig eigenval.xvg Input, Opt. xvgr/xmgr file -eig2 eigenval2.xvg Input, Opt. xvgr/xmgr file -comp eigcomp.xvg Output, Opt. xvgr/xmgr file -rmsf eigrmsf.xvg Output, Opt. xvgr/xmgr file -proj proj.xvg Output, Opt. xvgr/xmgr file -2d 2dproj.xvg Output, Opt. xvgr/xmgr file -3d 3dproj.pdb Output, Opt. Structure file: gro g96 pdb etc. -filt filtered.xtc Output, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -extr extreme.pdb Output, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -overoverlap_atp-atp.xvg Output, Opt! xvgr/xmgr file -inprinprod.xpm Output, Opt. X PixMap compatible matrix file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -tu enum ps Time unit: fs, ps, ns, us, ms or s -[no]w bool no View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -first int1 First eigenvector for analysis (-1 is select) -lastint8 Last eigenvector for analysis (-1 is till the last) -skipint1 Only analyse every nr-th frame -max real 0 Maximum for projection of the eigenvector on the average structure, max=0 gives the extremes -nframes int2 Number of frames for the extremes output -[no]split bool no Split eigenvector projections where time is zero -[no]entropy bool no Compute entropy according to the Quasiharmonic formula or Schlitter's method. -tempreal 298.15 Temperature for entropy calculations -nevskip int6 Number of eigenvalues to skip when computing the entropy due to the quasi harmonic approximation. When you do a rotational and/or translational fit prior to the covariance analysis, you get 3 or 6
[gmx-users] Orders of the residues in gromacs
Hi, You are probably mixing resid and residue. In VMD, - resid is taken as found in the file (pdb, gro, etc). You may have several residues with the same resid if you load a file with multiple chains. - residue is generated internally by VMD, it is incremented by one unit for each residue, even if there are gaps in the sequence, it always starts at 0 and is granted to be unique for each residue. Cheers, Rui Rodrigues De: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] Em Nome De Du Jiangfeng (BIOCH) [j...@maastrichtuniversity.nl] Enviado: sexta-feira, 3 de Fevereiro de 2012 9:06 Para: gmx-users@gromacs.org Assunto: [gmx-users] RE: gmx-users Digest, Vol 94, Issue 24 Dear All, I found a strange thing about VMD. When I use mouse label residue from graph (Mouse -- Label -- Atom), i would get a correct residue as it is in .gro file, while when I use graphics -- representations -- selections, then the residue selected here is totally different with the one which has the same number in the .gro file. Be careful with it, everybody. Jiangfeng. Jiangfeng Du, PhD Student Cardiovascular Research Institute Maastricht Department of Biochemistry P.O. Box 616 Mobile: +31-681741859 FAX: +31-43-3884159 6200 MD Maastricht The Netherlands Dear Friends, I want to measure some data of a special residue, for instance TRP143, from my MD result. But i encountered a problem. The residue number 143 is ordered in .gro file, while it seems the residue orders is random in gromacs. It points to another residue when I specify residue number 143 in VMD or when I am using make_ndx program ( -- r 143; q). Apparently, gromacs numbering system is not based on the orders in the .gro structure file. Does anybody know how to link the gromacs order to the structure file's order correctly? Thank you in advance, Jiangfeng. Jiangfeng Du, PhD Student Cardiovascular Research Institute Maastricht Department of Biochemistry P.O. Box 616 Mobile: +31-681741859 FAX: +31-43-3884159 6200 MD Maastricht The Netherlands -- Message: 4 Date: Thu, 02 Feb 2012 12:43:17 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Orders of the residues in gromacs To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4f2acb35.8050...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Du Jiangfeng (BIOCH) wrote: Dear Friends, I want to measure some data of a special residue, for instance TRP143, from my MD result. But i encountered a problem. The residue number 143 is ordered in .gro file, while it seems the residue orders is random in gromacs. It points to another residue when I specify residue number 143 in VMD or when I am using make_ndx program ( -- r 143; q). Apparently, gromacs numbering system is not based on the orders in the .gro structure file. Does anybody know how to link the gromacs order to the structure file's order correctly? Depending on the Gromacs version you're using, residue numbering is treated differently. In pdb2gmx, you can choose to renumber the residues from 1 or not. The default is to not renumber the file. You should check to see what you did with respect to this option and whether or not your coordinate file is numbered from 1. If it is not, then what you think is residue 143 may not be interpreted that way by all external programs, depending on whether or not they respect the numbering of the .gro file. -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 -- Message: 8 Date: Fri, 3 Feb 2012 10:04:28 +0800 (SGT) From: Jianguo Li ljg...@yahoo.com.sg Subject: Re: [gmx-users] Orders of the residues in gromacs To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 1328234668.1600.yahoomail...@web190204.mail.sg3.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Another possible reason is due to vmd, which numbers the residue from 0. Residue 143 in gromacs corresponds to residue 142 in vmd. Cheers, Jianguo -- 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
