[gmx-users] g_dist output
John Shultz
jackygrahamez at gmail.com
Tue Mar 9 15:19:43 CET 2010
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 <jalemkul at 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 <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
>>>>>> posting!
>>>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>>>> interface
>>>>>> or send it to gmx-users-request at 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-users at 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-request at 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-users at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
--
John Shultz
202-494-1707
More information about the gromacs.org_gmx-users
mailing list