[gmx-users] -vsite and protein-ligand simulations
alec.zander at gmail.com
Fri Dec 20 22:15:52 CET 2013
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.
The -vsite modifed .gro files show weird extra points on the hydrogen
bearing groups affected when viewed in VMD.
I don't know what to say ... I'm afraid GROMACS will call me stupid if I
make another mistake. They should make GROMACS say nice encouraging things
all the time. But I don't mind, I have gotten to stage where GROMACS is
starting to be fun.
Thanks for your help!
On Fri, Dec 20, 2013 at 2:46 PM, Justin Lemkul [via GROMACS] <
ml-node+s5086n5013467h99 at n6.nabble.com> wrote:
> On 12/20/13 12:24 PM, unitALX wrote:
> > Hello again!
> > Another question about -vsite:
> > does *-vsite aromatics * also include the hydrogens that could be
> > virtualized by *-vsite hydrogens*? Or should I say *-vsite hydrogens
> > aromatics* to virtualize both?
> -vsite hydrogens should also encompass aromatics, but -vsite aromatics
> will not
> convert all hydrogens. The -vsite option only takes one string. Of
> course, one
> could execute the commands and have a definitive answer in seconds ;)
> 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
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