Re: Speeding up: Dummy constructions for aromatics or hydrogens

From: Axel Kohlmeyer (
Date: Fri Apr 17 2009 - 16:05:34 CDT

On Sat, 2009-04-18 at 00:50 +0400, DimitryASuplatov wrote:
> Thank you for answering.
> >> I`ve been using gromacs previously. It is generaly a default strategy in
> >> gmx to use dummy constructions for hydrogens or aromatics and heavy
> >> hydrogens constructions. This enables fast and reliable calculations
> >> with up to 4fs.
> >
> > hmm... "constructions" sounds strange. i have not seen
> > this in the gromacs documentation, either.
> > are you talking about "constraints"?
> >
> I meant "dummy atoms" for aromatics or hydrogens. It is -vsite
> aromatics/hydrogens option for pdb2gmx.
> Is it the same as "rigidBonds" in namd?

no. it is equivalent to the "constraints" flag in gromacs' .mdp file.

with multi-timestepping, you can have a much larger "outer" timestep,
so i don't think it is really needed to have these virtual sites,
unless you go to (proper?) coarse graining (which is supported via
a conversion tool in VMD).



> Thanks

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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