[gmx-users] -vsite hydrogen

Justin Lemkul jalemkul at vt.edu
Mon Dec 29 16:28:01 CET 2014

On 12/29/14 6:28 AM, h.alizadeh at znu.ac.ir wrote:
> Dear Users,
> I am simulating a membrane protein with charmm ff with a 2fs time step.
> How the results will be affected if I use a 5fs time step by using "-vsite
> hydrogen" option in pdb2gmx? Do my results loose their accuracy if I use
> this option?

Well, it's easy to test.  The membrane properties that are expected to be 
observed are very easy to quantify.  We didn't test our CHARMM36 port with 
virtual sites at all, so we cannot recommend such usage.  Test thoroughly before 
doing any real production work.  Membranes are extremely sensitive to alteration.



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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