[gmx-users] PBC correction to visualize a protein-membrane structure

Justin Lemkul jalemkul at vt.edu
Sat May 17 22:36:45 CEST 2014

On 5/17/14, 5:49 AM, Juan Munoz-Garcia wrote:
> Dear Mark,
> I’ve used numbers. Just indicated them as x_box/2, etc to be clearer.

There are two possibilities:

1. You built the system wrong and trjconv can't fix it.  Without the full 
sequence of commands used to build the system, no one can provide any advice 
here.  Providing an image that shows the unit cell ("pbc box" in the Tcl window 
in VMD) can also be informative in this regard.

2. This is a PBC issue that should be resolvable, probably within a few 
iterations of trjconv.  See 
  Often times, it helps to start with a new .tpr file that has the system 
centered properly when remove jumps, etc.



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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