[gmx-users] Stop protein diffusion in simulation box to make a movie
jalemkul at vt.edu
Sat Dec 13 15:36:35 CET 2014
On 12/13/14 6:04 AM, Hassan Aaryapour wrote:
> Dear Gromacs Users,
> I made a trajectory movie using VMD and smoothing increased for
> getting the residues motion slower, but the protein is translate and
> diffuse in box, and causes very hard of seeing and analyzing how
> ligand structure changes during simulation. How can I stop the protein
> translation and following ligand motion easier?
For a simple case like this, centering and subsequent rotational+translational
fitting is all you should need.
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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