[gmx-users] -vsite and protein-ligand simulations

Justin Lemkul jalemkul at vt.edu
Fri Dec 20 18:25:41 CET 2013

On 12/20/13 8:14 AM, Alec Zander wrote:
> Hello!
> I'm pretty new to Gromacs. I'm running Gromacs 4.6.5 and I've been trying
> out the -vsite aromatics on my protein to achieve a 4fs timestep, and I am
> happy with the results. Can -vsite also be used for ligands in a ligand +
> protein simulation? Would this introduce any problems with ligand behavior
> differing from its parameterization?

You can assign virtual sites to whatever species you like.  I would assume you 
would see instability with a large time step and molecules that didn't have 
virtual sites.  It would be wise, of course, to demonstrate that your 
molecule(s) of interest behave correctly with and without virtual sites.



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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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