[gmx-users] sridhar at dummy hydrogens in pdb2gmx.
feenstra at chem.vu.nl
Fri May 2 09:04:00 CEST 2003
> Dear Anton Feenstra,
> Yes, I have used the option dummy hydrogens in pdb2gmx. I did not know it
> creates constraints and So, for CG minimization this option should not be
> used. But I learnt that "dummy hydrogens" option speeds up the program.
It does for dynamics (MD), not for energy minimization (EM). The speed-up
can be achieved by choosing a larger time step in MD (e.g. 5 fs in stead of
the usual 2 fs), as per my J.Comput.Chem. 20, 786-798 (1999) paper. As
there is no time in EM, there is no possibility for this kind of speed-up.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
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