[gmx-developers] Incorrect simulation?

[Erik Lindahl]

Hi Scott,

>
> It looks like you were right, the model is designed to rely on the
> stochastic kicks for solvent-like behavior.  Good call.
>
> I'm looking for something to simulate in a vaccum (i.e. not a lot of
> atoms) that has some visual aspect that is easy to see by the general
> public for a demo.  The tRNA example is good, but the sd integrator
> might be hard to implement.

integrator = sd

The details on how to specify the strength of the stochastic  
component are in the manual and mdp file documentation :-)

Cheers,

Erik


-----------------------------------------------------------
Erik Lindahl  <lindahl at sbc.su.se>
Assistant Professor, Stockholm Bioinformatics Center
Stockholm University, SE 106 91 Stockholm
Phone: +46 8 5537 8564     Fax: +46 8 5537 8214




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