[gmx-users] Stop protein diffusion in simulation box to make a movie

[Justin Lemkul]

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?
>

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow

For a simple case like this, centering and subsequent rotational+translational 
fitting is all you should need.

-Justin

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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
http://mackerell.umaryland.edu/~jalemkul

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