[gmx-users] g_dist output
Justin A. Lemkul
jalemkul at vt.edu
Tue Mar 9 15:11:51 CET 2010
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 <jackygrahamez at 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 <jalemkul at 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 <jalemkul at 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-users at gromacs.org
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>> Please search the archive at http://www.gromacs.org/search before
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>>>>>
>>>>
>>>>
>>> --
>>> ========================================
>>>
>>> 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-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before posting!
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>>>
>>
>>
>> --
>> 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
========================================
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