[gmx-users] shift in trajectory

[Amin Rouy]

Dear Justin,

Yes, they form a clear phase separation.
Well, I did not clearly understand your last suggestion. I do not need to
have their COM coordinate, I need COM of 'A' stays in the middle of the
box.

On Thu, Oct 17, 2019 at 5:17 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/17/19 8:04 AM, Amin Rouy wrote:
> > Dear Justin,
> >
> > I have a two-component system (they demix), which are grouped as  'A' and
> > 'B' from beginning of the simulation. Now my trajectory is asymmetric
> with
> > respect to the center. I can make it symmetric with gmx trjconv flag
> -shift
> > manually, but I need to apply the flag -center to get the 'A' component
> > sitting exactly at the center of the box.
> >
> > So having my index file, what I do is:
> >
> > 1- *gmx trjconv -f NPT.xtc -o NPT-centered.xtc -pbc none -n index.ndx*
> >
> > and I select whole system.
>
> Making molecules whole should always be the first step. I disagree with
> the previous advice you were given to use this PBC option first.
>
> >
> > 2- *gmx trjconv -f NPT-centered.xtc -o NPT-centered2.xtc -n index.ndx
> > -center*
> >
> > and I select group 'A' for Select group for centering, and whole system
> for
> > Select group for output.
> >
> > 3- *gmx trjconv -f NPT-centered2.xtc -o NPT-centered3.xtc -n index.ndx
> -pbc
> > mol -s NPT.tpr *
> >
> > and here I select whole system.
> >
> >
> > What I get is the same trajectory as I had in the beginning, no change at
> > all. I can see it with vitalizing and moreover from gmx density outcome.
>
> Do you get a clear phase separation with a layer of A and a layer of B
> in the simulation? In steps prior to separation, it will not be apparent
> that the molecules are actually centered, but you can obtain their COM
> coordinates with gmx traj -ox -com and confirm that they correspond to
> the box center.
>
> -Justin
>
> --
> ==================================================
>
> 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
>
> ==================================================
>
> --
> 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.
>