[gmx-users] Broken lipid molecules

Justin Lemkul jalemkul at vt.edu
Sat Sep 21 04:36:29 CEST 2013

On 9/20/13 5:21 PM, Rama wrote:
> HI,
> At the end of a MD run, the lipid molecules in a membrane protein are
> broken. I load .gro and .trr file into VMD to watch MD simulations, the
> lipids are broken at periodic boundaries.
> I try to fix it by trjconv -pbc nojump but output came with only 2 frames
> but initially it was 1500 frames.

Either something is wrong with the trajectory or something is wrong with the 
command you gave.  Based on the information at hand, no one can say.

> How to fix whole MD trajectory?

trjconv -pbc mol



Justin A. Lemkul, Ph.D.
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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