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

[unitALX]

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
>
> --
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