[gmx-users] shift in trajectory

[Patel, Lara Anne]

Have you tried using the -center flag with -pbc mol for example:


gmx trjconv -f traj.xtc -o traj-centered.xtc -center -pbc mol -n index.ndx


The reason to give the index file is so that you can select the group that you are centering by.  If you do not have the residue's A as a seperate group in the index file, you should start by producing an index file with your centering group isolated and then another group for what you will want to be printing in your new trajectory file.


There is one small caveate to the centering algorithm though: There are two ways that the center of mass of an object can be in the middle of the simulation box.

  1) The mass is in the center of the box.

  2) The mass is split on opposite ends of the box.

The last time I was using the -center function of the trjconv function, it would alternate between the two. I am not sure if this has been fixed.


Is the second option what you have been seeing?


Best Regards,

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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