[gmx-users] g_dist output
John Shultz
jackygrahamez at gmail.com
Tue Mar 9 15:03:25 CET 2010
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
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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
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