[gmx-users] shift in trajectory

[Justin Lemkul]

On 10/16/19 12:00 PM, Patel, Lara Anne wrote:
> There is a way to get around the mass being split across the simulation box IF your residue A's are all grouped together from the start.
>
>
> First, run the gmx trjconv function with -pbc flag as none.  The trajectory produced will be spread out.  The index group selected should be for the whole of what you will be printing out in your final trajectory.
>
> gmx trjconv -f traj.xtc -o traj1.xtc -pbc none -n index.ndx
>
>
>
> Second run the gmx trjconv function with the -center command with an index file that has a group just for residue 'A'.  The index group selected for centering should be for residue A. The program will also ask for what group will be printed to the file (i.e. your system).
>
> gmx trjconv -f traj1.xtc -o traj2.xtc -n index.ndx -center
>
>
>
> Third run the gmx trjconv function with the -pbc flag for mol to get everything back within the periodic boundary conditions.  This will only ask for the group that should be printed.
>
> gmx trjconv -f traj2.xtc -o traj2.xtc -n index.ndx -pbc mol
>
>
> You might be able to combine the second and third steps but I find that it is easier just to do this in progressive steps.

Making molecules whole should always be the first step. See 
http://manual.gromacs.org/current/user-guide/terminology.html#suggested-workflow

One call to trjconv is all the OP needs, using -pbc mol -center and an 
index group corresponding to the residue of interest to be chosen for 
centering.

-Justin

>
> Lara
>
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Amin Rouy <aminrou1986 at gmail.com>
> Sent: Wednesday, October 16, 2019 9:19:39 AM
> To: gromacs.org_gmx-users at maillist.sys.kth.se; gmx-users at gromacs.org
> Subject: [gmx-users] shift in trajectory
>
> Hi,
>
> I want to shift my trajectory such that the center of mass of residue 'A'
> locates in the center of my rectangular box.
>
> I have tries all flags in  gmx trjconv, but could not succeed. Any help
> would be appreciated.
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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