Re: Speeding up: Dummy constructions for aromatics or hydrogens

From: Axel Kohlmeyer (
Date: Fri Apr 17 2009 - 15:22:04 CDT

On Fri, 2009-04-17 at 21:11 +0400, DimitryASuplatov wrote:
> Hello,

hello dimitry,

> 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"?

> 1/ Is it possible to set dummy constructions in namd? How? I did not
> find anything appropriate in the manual or on the web

yes. check out the rigidBonds keyword.
the atomic mass is set in the .psf file.

> 2/ What are the general strategies to speed up the calculations in namd?

the main, hardware independent method is to use multi-timestepping
via r-RESPA. for details, please see the user's guide. the upcoming
2.7 release will also include hardware specific optimizations
(e.g. SIMD or GPU kernels for non-bonded interactions).


> Thanks, I appreciate your time.

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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