[gmx-users] Removing fastest degrees of freedom

[Anton Feenstra]

Ghermes Chilov wrote:
> Hi!
> 
> I'd like to ask Gromacs's gurus (especially Anton F.) one technical
> question concerning dummifying hydrogens and aromatics (and making
> the remaning hydrogens havier) in order to increase the integration
> time step:
> 
> should i introduce extra bond (or constraint type 2) between serine
> (tyrosine, threonine) hydroxyle and proper carbon atom in ff**.rtp?

No, 'pdb2gmx -dummy hydrogens' does that for you.

IIRC, David vd Spoel recently wrote an article where he compared (long)
simulations with and w/o 'dummy hydrogens', showing no significant
differences.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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