[gmx-users] trjconv -pbc nojump

Reisser, Sabine (IPC) sabine.reisser at kit.edu
Thu Sep 3 10:31:17 CEST 2015

Thanks, I found that there is an option -nojump also for g_traj, which I use to get the average height. That solves the problem for my purpose.


Dr. Sabine Reißer
Theoretical Chemical Biology
Institute of Physical Chemistry
Karlsruhe Institute of Technology

Von: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> im Auftrag von Justin Lemkul <jalemkul at vt.edu>
Gesendet: Mittwoch, 2. September 2015 22:40
An: gmx-users at gromacs.org
Betreff: Re: [gmx-users] trjconv -pbc nojump

On 9/2/15 9:36 AM, Reisser, Sabine (IPC) wrote:
> Well, in the end I would like to have an average value for the P atoms of
> each leaflet. I know which lipids belong to which leaflet, but I need to
> avoid box jumps along z, otherwise I will obviously get a wrong average.
> Using first trjconv  -pbc whole and then -pbc nojump actually seems to work
> in the way that molecules don't jump in z anymore. However, they are not
> whole anymore. Also, I would like all lipids of one leaflet on one side of

Once made whole, I don't understand how they would have further problems.  Make
sure your reference structure in the .tpr passed to -s has whole molecules that
are all in the box as a proper reference.

> the box. Now, the lipids upper edge is at the box edge, and some have jumped
> to the lower box edge. I thought maybe with -pbc cluster I could fix this.
> Otherwise I have to shift the molecules which are jumped (already in the
> starting structure) manually by the box height.

This can be overcome with the -trans (in concert with -pbc mol) and/or -center



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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