[gmx-users] shift in trajectory

[Patel, Lara Anne]

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.


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.
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.