I tried a couple of things according to your suggestions, but no
luck so far
I used the following commands
1) trjconv -f trajout_dt2000.xtc -s topol.tpr -pbc mol -o
trajout_mol.xtc
2) trjconv -f trajout_mol.xtc -s topol.tpr -pbc nojump
trajout_nojump.xtc
no luck...If I use command 1) only the trajout_mol.xtc the protein
is still "split" into to across 2 boxes ie it looks like it did not
do anything to the trajectory
if I use 1) and 2) the system gets "ripped" apart. The system is no
longer a box but a flat disk (very funky)
then I tried
trjconv -f trajout_dt2000.xtc -s topol.tpr -pbc mol -fit
translation -o trajout_fit.xtc
again...it looks like the trajectory did not change and the protein
is still jumping out of the box
then I tried
trjconv -f trajout_dt2000.xtc -s topol.tpr -pbc mol -trans -6 6 0 -
o trajout_trans.xtc (the box is about 12 x 12)
now at least this command did something to the trajectory. The
entire protein is now in the center of the box (rather than in the
corner) but in the frames where the pb jump occurs the protein still
jumps out of the box! it now simply jumps from the center to the
next box rather than "sliding" across the border into the next box
On 21 February 2011 16:02, <gmx-users-requ...@gromacs.org> wrote:
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Today's Topics:
1. Re: g_covar to calculate correlation of motion (Tsjerk Wassenaar)
2. Re: g_covar to calculate correlation of motion (bipin singh)
3. removing pbc jumps from trajectory (Evelyne Deplazes)
4. Re: removing pbc jumps from trajectory (XAvier Periole)
---------- Forwarded message ----------
From: Tsjerk Wassenaar <tsje...@gmail.com>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Date: Mon, 21 Feb 2011 08:14:26 +0100
Subject: Re: [gmx-users] g_covar to calculate correlation of motion
Hi Bipin,
Try using a .gro or .pdb file as reference structure (-s). Only .tpr
files are version specific.
Cheers,
Tsjerk
On Feb 21, 2011 8:05 AM, "bipin singh" <bipinel...@gmail.com> wrote:
Dear GMX users,
I want to calculate the correlated motion between atoms during the
md simulation
for that purpose I am using g_covar(the one which is available
under http://www.gromacs.org/Downloads/User_contributions/Other_software)
but it is not compatible with the GROMACS-4.5.3, so please suggest
me the alternative way or does anyone have the modified g_covar for
GROMKACS-4.5.3.
--
---------------------------------
Thanks and regards
Bipin Singh
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---------- Forwarded message ----------
From: bipin singh <bipinel...@gmail.com>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Date: Mon, 21 Feb 2011 13:17:48 +0530
Subject: Re: [gmx-users] g_covar to calculate correlation of motion
Hi,
Thanks for your suggestion.
While running the g_covar it is showing the error that
aminoacids.dat is not found, so i have copied the
residuetypes.dat(which i seems the new modified name for
aminoacids.dat in current GROMACS version), then it prompts to
choose the group for least square fit, which is not usual groups(i.e
protein or C alpha groups etc.).....please suggest where i have made
mistake.
Choose a group for the least squares fit
Opening library file aminoacids.dat
WARNING 2 [file aminoacids.dat, line 1]:
File aminoacids.dat is empty
Group 0 ( System) has 30585 elements
Group 1 ( GLU) has 47 elements
Group 2 ( HIS) has 86 elements
Group 3 ( ASN) has 224 elements
Group 4 ( PRO) has 56 elements
Group 5 ( VAL) has 272 elements
Group 6 ( MET) has 68 elements
Group 7 ( GLY) has 168 elements
Group 8 ( ILE) has 190 elements
Group 9 ( ALA) has 110 elements
Group 10 ( SER) has 143 elements
Group 11 ( PHE) has 80 elements
Group 12 ( LYS) has 242 elements
Group 13 ( TYR) has 189 elements
Group 14 ( LEU) has 304 elements
Group 15 ( GLN) has 102 elements
Group 16 ( TRP) has 48 elements
Group 17 ( ARG) has 120 elements
Group 18 ( ASP) has 108 elements
Group 19 ( THR) has 141 elements
Group 20 ( SOL) has 27882 elements
Group 21 ( CL) has 5 elements
On Mon, Feb 21, 2011 at 12:44, Tsjerk Wassenaar <tsje...@gmail.com>
wrote:
Hi Bipin,
Try using a .gro or .pdb file as reference structure (-s). Only .tpr
files are version specific.
Cheers,
Tsjerk
On Feb 21, 2011 8:05 AM, "bipin singh" <bipinel...@gmail.com> wrote:
Dear GMX users,
I want to calculate the correlated motion between atoms during the
md simulation
for that purpose I am using g_covar(the one which is available
under http://www.gromacs.org/Downloads/User_contributions/Other_software)
but it is not compatible with the GROMACS-4.5.3, so please suggest
me the alternative way or does anyone have the modified g_covar for
GROMKACS-4.5.3.
--
---------------------------------
Thanks and regards
Bipin Singh
--
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---------------------------------
Thanks and regards
Bipin Singh
---------- Forwarded message ----------
From: Evelyne Deplazes <depla...@student.uwa.edu.au>
To: gmx-users@gromacs.org
Date: Mon, 21 Feb 2011 15:52:38 +0800
Subject: [gmx-users] removing pbc jumps from trajectory
Hi
I have a series of trajectories from a coarse grained simulation
(Martini force field) that I ran using gromacs 4.0.4. The system
consists of a protein embedded in a POPC bilayer solvated with
water. During the simulation the protein (most of time its actually
*part* of the protein) jumps across the pb into the neighboring box.
I use a series of tcl scripts to analyse my trajectories and for
that purpose I need to remove that "period boundary jump" and make
the protein "whole" again.
I have tried the approach described on the gromacs website
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
I also other combinations of -whole, -center and -pbc nojump of
trjconv, without any luck. Can anyone suggest how I can re-center
the protein and remove the pb jump ie make the protein "whole"
Thanks
Evelyne
--
Evelyne Deplazes
PhD student
Theoretical Chemistry group
University of Western Australia
---------- Forwarded message ----------
From: XAvier Periole <x.peri...@rug.nl>
To: "depla...@student.uwa.edu.au" <depla...@student.uwa.edu.au>,
Discussion list for GROMACS users <gmx-users@gromacs.org>
Date: Mon, 21 Feb 2011 09:01:54 +0100
Subject: Re: [gmx-users] removing pbc jumps from trajectory
You have to make sure of two things:
1- use a reference (gro or tpr) where the molecule is whole! The tpr
is prefered since the molecules are defined.
2- with such a reference and the option -mol you'll get a trajectory
with the protein as a whole.
On that trajectory you may apply more modifications:
-nojump with generate a trajectory where the pbc are not applied so
you can do msd analysis. Note that thisnis done by default in g_msd.
- fitting with only translation removed (equivalent to centering but
more stable. Centering works strangely)
XAvier.
On Feb 21, 2011, at 8:52, Evelyne Deplazes <depla...@student.uwa.edu.au
> wrote:
Hi
I have a series of trajectories from a coarse grained simulation
(Martini force field) that I ran using gromacs 4.0.4. The system
consists of a protein embedded in a POPC bilayer solvated with
water. During the simulation the protein (most of time its actually
*part* of the protein) jumps across the pb into the neighboring
box. I use a series of tcl scripts to analyse my trajectories and
for that purpose I need to remove that "period boundary jump" and
make the protein "whole" again.
I have tried the approach described on the gromacs website
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
I also other combinations of -whole, -center and -pbc nojump of
trjconv, without any luck. Can anyone suggest how I can re-center
the protein and remove the pb jump ie make the protein "whole"
Thanks
Evelyne
--
Evelyne Deplazes
PhD student
Theoretical Chemistry group
University of Western Australia
--
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--
Evelyne Deplazes
PhD student
Theoretical Chemistry group
University of Western Australia
--
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