[gmx-users] Performance

[M.Naser]

Hi Anton,

Thank you very much for your response. Which constrian algorithm would you
advise to use, shake or lincs?

Another basic question: how the system propagate in Gromacs? - is it on
the basis of atoms or centre of mass?

With regards,

Abu

> 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) *
>
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> |  _   _  ___,| K. Anton Feenstra                                     |
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