[gmx-users] on VMD analysis of the gromacs production MD

Justin Lemkul jalemkul at vt.edu
Sun Jul 12 17:10:15 CEST 2015

On 7/11/15 8:45 PM, Brett wrote:
> Dear All,
> After energy minimization, 100 ps NVT md and 100 ps NPT md (based on the
> on-line lysozyme tutorial), I have processed a 30 ns production MD (also
> based on the on-line lysozyme tutorial). Then I load the NPT.gro and the
> 30ns_production_md.xtc to the VMD, and by VMD I find in the whole 30 ns md,
> the whole protein molecule has an about 50 degree rotation (the 50 degree
> occurs gradually in the 15 ns md, not a sudden 50 degree rotation). Is this
> 50 degree rotation normal or abnormal?

Molecules diffuse.  That's why it's called "molecular dynamics" and not 
"molecular static structures."

> If by VMD I want to observe the local conformation changes in the whole 30 ns
> md, rather than the  global 50 degree rotation, will you please tell me which
> trajectory file I need to load to VMD, and by which command I can get that
> trajectory file?

trjconv provides several methods for fitting to remove global 
translation/rotation.  See the help information.



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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