John Shultz 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.
The .tpr file is required input for g_dist, but the frame(s) actually analyzed
are in the generic trajectory file passed to the -f flag. Both the .tpr and
trajectory are required input. This trajectory can be .xtc, .trr, .gro, .pdb,
or a few others. The program uses information about the atoms in the .tpr file
to carry out the analysis on the trajectory. As you've shown, you pass "md.gro"
to g_dist, so you will only ever have that .gro file's information. While it is
possible to write the entire trajectory in .gro format, this is very
inconvenient, since the file size gets large in a hurry, so I assume your
"md.gro" is just a single frame, so you're getting exactly what you should
expect. If you want distances over time, pass a .xtc or .trr to the -f option
of g_dist.
-Justin
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 <[email protected]> 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 <[email protected]> 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
========================================
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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
========================================
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