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

Justin Lemkul jalemkul at vt.edu
Fri Dec 20 22:55:50 CET 2013

On 12/20/13 4:14 PM, unitALX wrote:
> Its true, so I did it!  and looked at the resulting .gro files in VMD.
> I saw that
>        *-vsite hydrogen *virtualizes only the non-aromatic hydrogens
>        *-vsite aromatics *virtualizes all hydrogens, aromatic and otherwise.
> I guess therefore that one cannot, for example, virtualize *only* the
> aromatic hydrogens, as passing the *aromatics *option seems to virtualize
> all the others too.

So to clarify, using "-vsite hydrogens" adds virtual sites for all hydrogen 
atoms, including those on aromatic rings.  Using "-vsite aromatics" virtualizes 
ALL atoms of the aromatic ring, hydrogens included.  So no, it is not possible 
to virtualize aromatic hydrogens and nothing else.

> The -vsite modifed .gro files show weird extra points on the hydrogen
> bearing groups affected when viewed in VMD.

Those "weird extra points" are the virtual sites that you told pdb2gmx to produce.



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


More information about the gromacs.org_gmx-users mailing list