[gmx-users] shift in trajectory

[Amin Rouy]

Dear Justin,

Thank you for detailed answer. However, I am still struggling and none of
these helped me.

One thing I concern in traj.tpr file;
 I run gmx trjconv with Gromcac.5, which requires .tpr file, while I see in
http://manual.gromacs.org/documentation/2019/onlinehelp/gmx-trjconv.html that
the file is 'Optional' to provide.

On Wed, Oct 16, 2019 at 6:05 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
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>
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>
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