Thank you Justin. The LIG was missing from our default mdp parameters. That explains why we could not use the xtc file. I am adding it now.
On Tue, Mar 9, 2010 at 9:11 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > John Shultz wrote: >> >> I tried using the xtc instead but it says the atom range is outside the >> index >> > > Well, 3868 is the number of atoms in your protein, so I'm guessing you set > "xtc_grps = Protein" in the .mdp file. If you want to analyze other groups, > then you have to actually save their coordinates when running your MD. > > -Justin > >> >> g_dist -f md.xtc -s md.tpr -n index.ndx < protein_lig.txt >> :-) G R O M A C S (-: >> >> Gallium Rubidium Oxygen Manganese Argon Carbon Silicon >> >> :-) VERSION 4.0.5 (-: >> >> >> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. >> Copyright (c) 1991-2000, University of Groningen, The Netherlands. >> Copyright (c) 2001-2008, The GROMACS development team, >> check out http://www.gromacs.org for more information. >> >> This program is free software; you can redistribute it and/or >> modify it under the terms of the GNU General Public License >> as published by the Free Software Foundation; either version 2 >> of the License, or (at your option) any later version. >> >> :-) g_dist (-: >> >> Option Filename Type Description >> ------------------------------------------------------------ >> -f md.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt >> -s md.tpr Input Run input file: tpr tpb tpa >> -n index.ndx Input, Opt! Index file >> -o dist.xvg Output, Opt. xvgr/xmgr file >> -lt lifetime.xvg Output, Opt. xvgr/xmgr file >> >> Option Type Value Description >> ------------------------------------------------------ >> -[no]h bool no Print help info and quit >> -nice int 19 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) >> -[no]xvgr bool yes Add specific codes (legends etc.) in the >> output >> xvg files for the xmgrace program >> -dist real 0 Print all atoms in group 2 closer than dist to >> the center of mass of group 1 >> >> Reading file md.tpr, VERSION 4.0.5 (single precision) >> Group 0 ( System) has 38210 elements >> Group 1 ( Protein) has 3868 elements >> Group 2 ( Protein-H) has 1980 elements >> Group 3 ( C-alpha) has 244 elements >> Group 4 ( Backbone) has 732 elements >> Group 5 ( MainChain) has 974 elements >> Group 6 (MainChain+Cb) has 1206 elements >> Group 7 ( MainChain+H) has 1198 elements >> Group 8 ( SideChain) has 2670 elements >> Group 9 ( SideChain-H) has 1006 elements >> Group 10 ( Prot-Masses) has 3868 elements >> Group 11 ( Non-Protein) has 34342 elements >> Group 12 ( LIG) has 46 elements >> Group 13 ( SOL) has 34212 elements >> Group 14 ( Na) has 48 elements >> Group 15 ( Cl) has 36 elements >> Group 16 ( Other) has 34342 elements >> Select a group: Selected 1: 'Protein' >> Select a group: Selected 12: 'LIG' >> Reading frame 0 time 0.000 >> ------------------------------------------------------- >> Program g_dist, VERSION 4.0.5 >> Source code file: gmx_dist.c, line: 165 >> >> Fatal error: >> Atom number 3914 in an index group is larger than number of atoms in >> the trajectory (3868) >> >> ------------------------------------------------------- >> >> "Shaken, not Stirred" (J. Bond) >> >> >> On Tue, Mar 9, 2010 at 9:03 AM, John Shultz <jackygraha...@gmail.com> >> wrote: >>> >>> Here is what our script is doing. It looks to me like we are analyzing >>> the tpr when we should be checking the xtc or trr if I understand you >>> correctly. And if we look at the trajectory we can measure the drift >>> for the entire simulation rather than a specific instance. >>> >>> >>> make_ndx -f md.tpr < make_ndx.txt >>> :-) G R O M A C S (-: >>> >>> GROup of MAchos and Cynical Suckers >>> >>> :-) VERSION 4.0.5 (-: >>> >>> >>> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. >>> Copyright (c) 1991-2000, University of Groningen, The Netherlands. >>> Copyright (c) 2001-2008, The GROMACS development team, >>> check out http://www.gromacs.org for more information. >>> >>> This program is free software; you can redistribute it and/or >>> modify it under the terms of the GNU General Public License >>> as published by the Free Software Foundation; either version 2 >>> of the License, or (at your option) any later version. >>> >>> :-) make_ndx (-: >>> >>> Option Filename Type Description >>> ------------------------------------------------------------ >>> -f md.tpr Input, Opt! Structure file: gro g96 pdb tpr tpb tpa >>> -n index.ndx Input, Opt., Mult. Index file >>> -o index.ndx Output Index file >>> >>> Option Type Value Description >>> ------------------------------------------------------ >>> -[no]h bool no Print help info and quit >>> -nice int 0 Set the nicelevel >>> -natoms int 0 set number of atoms (default: read from >>> coordinate or index file) >>> >>> Reading file md.tpr, VERSION 4.0.5 (single precision) >>> >>> Reading structure file >>> Reading file md.tpr, VERSION 4.0.5 (single precision) >>> Going to read 0 old index file(s) >>> Analysing residue names: >>> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat >>> There are: 11489 OTHER residues >>> There are: 244 PROTEIN residues >>> There are: 0 DNA residues >>> Analysing Protein... >>> Analysing Other... >>> >>> 0 System : 38210 atoms >>> 1 Protein : 3868 atoms >>> 2 Protein-H : 1980 atoms >>> 3 C-alpha : 244 atoms >>> 4 Backbone : 732 atoms >>> 5 MainChain : 974 atoms >>> 6 MainChain+Cb : 1206 atoms >>> 7 MainChain+H : 1198 atoms >>> 8 SideChain : 2670 atoms >>> 9 SideChain-H : 1006 atoms >>> 10 Prot-Masses : 3868 atoms >>> 11 Non-Protein : 34342 atoms >>> 12 LIG : 46 atoms >>> 13 SOL : 34212 atoms >>> 14 Na : 48 atoms >>> 15 Cl : 36 atoms >>> 16 Other : 34342 atoms >>> >>> nr : group ! 'name' nr name 'splitch' nr Enter: list groups >>> 'a': atom & 'del' nr 'splitres' nr 'l': list residues >>> 't': atom type | 'keep' nr 'splitat' nr 'h': help >>> 'r': residue 'res' nr 'chain' char >>> "name": group 'case': case sensitive 'q': save and quit >>> >>> Copied index group 0 'System' >>> >>> Syntax error: "q " >>> >>> gcq#89: "This Doesn't Suck, It's a Black Hole !" (K.A. Feenstra) >>> >>> g_dist -f md.gro -s md.tpr -n index.ndx < protein_lig.txt >>> :-) G R O M A C S (-: >>> >>> GROup of MAchos and Cynical Suckers >>> >>> :-) VERSION 4.0.5 (-: >>> >>> >>> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. >>> Copyright (c) 1991-2000, University of Groningen, The Netherlands. >>> Copyright (c) 2001-2008, The GROMACS development team, >>> check out http://www.gromacs.org for more information. >>> >>> This program is free software; you can redistribute it and/or >>> modify it under the terms of the GNU General Public License >>> as published by the Free Software Foundation; either version 2 >>> of the License, or (at your option) any later version. >>> >>> :-) g_dist (-: >>> >>> Option Filename Type Description >>> ------------------------------------------------------------ >>> -f md.gro Input Trajectory: xtc trr trj gro g96 pdb cpt >>> -s md.tpr Input Run input file: tpr tpb tpa >>> -n index.ndx Input, Opt! Index file >>> -o dist.xvg Output, Opt. xvgr/xmgr file >>> -lt lifetime.xvg Output, Opt. xvgr/xmgr file >>> >>> Option Type Value Description >>> ------------------------------------------------------ >>> -[no]h bool no Print help info and quit >>> -nice int 19 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) >>> -[no]xvgr bool yes Add specific codes (legends etc.) in the >>> output >>> xvg files for the xmgrace program >>> -dist real 0 Print all atoms in group 2 closer than dist >>> to >>> the center of mass of group 1 >>> >>> Reading file md.tpr, VERSION 4.0.5 (single precision) >>> Group 0 ( System) has 38210 elements >>> Group 1 ( Protein) has 3868 elements >>> Group 2 ( Protein-H) has 1980 elements >>> Group 3 ( C-alpha) has 244 elements >>> Group 4 ( Backbone) has 732 elements >>> Group 5 ( MainChain) has 974 elements >>> Group 6 (MainChain+Cb) has 1206 elements >>> Group 7 ( MainChain+H) has 1198 elements >>> Group 8 ( SideChain) has 2670 elements >>> Group 9 ( SideChain-H) has 1006 elements >>> Group 10 ( Prot-Masses) has 3868 elements >>> Group 11 ( Non-Protein) has 34342 elements >>> Group 12 ( LIG) has 46 elements >>> Group 13 ( SOL) has 34212 elements >>> Group 14 ( Na) has 48 elements >>> Group 15 ( Cl) has 36 elements >>> Group 16 ( Other) has 34342 elements >>> Select a group: Selected 1: 'Protein' >>> Select a group: Selected 12: 'LIG' >>> Reading frames from gro file 'Protein in water', 38210 atoms. >>> Last frame 0 time 0.000 >>> >>> gcq#89: "This Doesn't Suck, It's a Black Hole !" (K.A. Feenstra) >>> >>> >>> # This file was created Tue Mar 9 13:58:58 2010 >>> # by the following command: >>> # g_dist -f md.gro -s md.tpr -n index.ndx >>> # >>> # g_dist is part of G R O M A C S: >>> # >>> # GROup of MAchos and Cynical Suckers >>> # >>> @ title "Distance" >>> @ xaxis label "Time (ps)" >>> @ yaxis label "Distance (nm)" >>> @TYPE xy >>> @ view 0.15, 0.15, 0.75, 0.85 >>> @ legend on >>> @ legend box on >>> @ legend loctype view >>> @ legend 0.78, 0.8 >>> @ legend length 2 >>> @ s0 legend "|d|" >>> @ s1 legend "d\sx\N" >>> @ s2 legend "d\sy\N" >>> @ s3 legend "d\sz\N" >>> 0.0000000 0.1572016 -0.1153002 -0.0301313 -0.1025198 >>> >>> >>> On Tue, Mar 9, 2010 at 8:46 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: >>>> >>>> John Shultz wrote: >>>>> >>>>> How come time is always 0.0000000 >>>>> >>>> You're analyzing a .gro file, so there is no time information stored. >>>> If >>>> you analyze a trajectory (i.e., .xtc or .trr), then the time is saved in >>>> the >>>> individual frames. >>>> >>>> -Justin >>>> >>>>> On Tue, Mar 9, 2010 at 8:16 AM, Justin A. Lemkul <jalem...@vt.edu> >>>>> wrote: >>>>>> >>>>>> John Shultz wrote: >>>>>>> >>>>>>> Hello, >>>>>>> >>>>>>> I am seeking clarification on what this output means. I believe it >>>>>>> says that the x axis is divided into 4 time intervals and they are >>>>>>> plotted against a y axis that measures total distance along all 3 >>>>>>> dimensional coordinates. >>>>>>> Am I reading this correctly? >>>>>>> >>>>>> There should be no decomposition of time intervals here. Distance is >>>>>> plotted continuously as a function of time. The first column is time, >>>>>> then >>>>>> the total distance, then each of the x, y, and z components of that >>>>>> distance. >>>>>> >>>>>> -Justin >>>>>> >>>>>>> # This file was created Sat Jan 30 00:20:03 2010 >>>>>>> # by the following command: >>>>>>> # g_dist -f md.gro -s md.tpr -n index.ndx >>>>>>> # >>>>>>> # g_dist is part of G R O M A C S: >>>>>>> # >>>>>>> # Glycine aRginine prOline Methionine Alanine Cystine Serine >>>>>>> # >>>>>>> @ title "Distance" >>>>>>> @ xaxis label "Time (ps)" >>>>>>> @ yaxis label "Distance (nm)" >>>>>>> @TYPE xy >>>>>>> @ view 0.15, 0.15, 0.75, 0.85 >>>>>>> @ legend on >>>>>>> @ legend box on >>>>>>> @ legend loctype view >>>>>>> @ legend 0.78, 0.8 >>>>>>> @ legend length 2 >>>>>>> @ s0 legend "|d|" >>>>>>> @ s1 legend "d\sx\N" >>>>>>> @ s2 legend "d\sy\N" >>>>>>> @ s3 legend "d\sz\N" >>>>>>> 0.0000000 0.0619448 0.0583303 0.0099401 -0.0183282 >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> -- >>>>>> ======================================== >>>>>> >>>>>> 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 list gmx-us...@gromacs.org >>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>>>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >>>>>> >>>>> >>>>> >>>> -- >>>> ======================================== >>>> >>>> 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 list gmx-us...@gromacs.org >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >>>> >>> >>> >>> -- >>> John Shultz >>> 202-494-1707 >>> >> >> >> > > -- > ======================================== > > 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 list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- John Shultz 202-494-1707 -- 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/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/mailing_lists/users.php