[gmx-users] Performance

[Anton Feenstra]

M.Naser wrote:
> Hi Anton,
> 
> Thanks for your very informative reply. What sort of contraint is normally
> used?

use:
dt = 0.002
and:
constraints = all-bonds

in your .mdp file

If you want more performance you can use the 'dummy atom' constructions 
David suggested. If you use pdb2gmx to generate your topology, you can 
use 'pdb2gmx -dummy hydrogens' to do that. You should also read (and 
cite, if you publish ;-) the following:

K. Anton Feenstra, Berk Hess and Herman J. C. Berendsen. Improving 
Efficiency of Large Time-scale Molecular Dynamics Simulations of 
Hydrogen-rich Systems. (1999) J. Comput. Chem. 20 (8), 786-798

(there is a link to the pdf file from my homepage...)


-- 
Groetjes,

Anton

* NOTE: New Phone & Fax numbers (below) *

  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 59 87608 - Fax: +31 20 59 87610           |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
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