[gmx-users] Broken lipid molecules

2013-09-20 Thread Rama 
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.

How to fix whole MD trajectory?

Thanks
Rama

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Re: [gmx-users] Broken lipid molecules

2013-09-20 Thread Justin Lemkul 



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

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==

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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