[gmx-users] shift in trajectory

[Amin Rouy]

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.

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.

On Thu, Oct 17, 2019 at 12:31 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/17/19 5:24 AM, Amin Rouy wrote:
> > Dear Justin,
> >
> > Thank you for detailed answer. However, I am still struggling and none of
> > these helped me.
>
> What have you done and what was the outcome? It's impossible to give
> better advice without knowing what specifically is going wrong.
>
> > 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.
>
> trjconv does a lot of things. Not all of them require a .tpr file, hence
> the "optional" designation. What you're trying to do does require a .tpr
> file because to account for periodicity effects, the bonded connectivity
> of all molecules needs to be known.
>
> -Justin
>
> >
> > 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.
> >>> --
> >>> 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
> >>>
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> >> send a mail to gmx-users-request at gromacs.org.
> >>
> >> --
> >> ==================================================
> >>
> >> 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
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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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
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