[gmx-users] g_dist output
John Shultz
jackygrahamez at gmail.com
Tue Mar 9 15:09:34 CET 2010
I tried using the xtc instead but it says the atom range is outside the index
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
>>>>
>>>> ========================================
>>>> --
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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
>
--
John Shultz
202-494-1707
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