[gmx-users] time step vs system

[Xavier Periole]

Nuno R. L. Ferreira wrote:

>Hi there
>
>Reading some papers about simulation of bilayer systems, it seams that the 
>max. recomended dt is about 5 fs.
>What about in systems with bilayer+protein?
>
>How can I know what's the max. dt for a specific system?
>
>  
>
For proteins I would not recommand using bigger than 2fs. Depends in the
problem your are addressing. People use more thant 2fs but the problems are
generaly about folding or large conformational space to explore. In 
those cases
the details are not that important. If your protein have to reorganize 
or adapt
to a contraint I would keep a 2fs time step.
In the case of bilayers, it is more like a solvent than like a protein. 
The interactions
are less sensitive thant in a protein and the properties are global and 
not much in
details.

XAvier

-- 
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   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: md.chem.rug.nl/~periole
   
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