[gmx-users] sridhar at dummy hydrogens in pdb2gmx.

[Anton Feenstra]

Mr.Sridhar wrote:
> 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.


-- 
Groetjes,

Anton
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|  _   _  ___,| K. Anton Feenstra                                     |
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