[gmx-users] Re: gmx-users Digest, Vol 82, Issue 150

Evelyne Deplazes deplae01 at student.uwa.edu.au
Mon Feb 21 09:45:08 CET 2011


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-request at gromacs.org> wrote:

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> Today's Topics:
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>   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 <tsjerkw at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at 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" <bipinelmat at 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
> *
> *
> *
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
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>
> ---------- Forwarded message ----------
> From: bipin singh <bipinelmat at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at 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 <tsjerkw at 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" <bipinelmat at 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
>> *
>> *
>> *
>>
>>
>> --
>> 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/Support/Mailing_Lists/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/Support/Mailing_Lists
>>
>>
>> --
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>
>
>
> --
> *
> ---------------------------------
> Thanks and regards
> Bipin Singh
> *
> *
> *
>
>
>
> ---------- Forwarded message ----------
> From: Evelyne Deplazes <deplae01 at student.uwa.edu.au>
> To: gmx-users at 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.periole at rug.nl>
> To: "deplae01 at student.uwa.edu.au" <deplae01 at student.uwa.edu.au>,
> Discussion list for GROMACS users <gmx-users at 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 <deplae01 at 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>
> 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
>
> --
> gmx-users mailing list     <gmx-users at gromacs.org>gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists>
> http://www.gromacs.org/Support/Mailing_Lists
>
>
> --
> 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/Support/Mailing_Lists/Search before posting!
>



-- 
Evelyne Deplazes

PhD student
Theoretical Chemistry group
University of Western Australia
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