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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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