[gmx-users] MD simulation on 1 and 4 nodes

[David van der Spoel]

On Wed, 2003-03-26 at 15:24, Alexander Zuev wrote:
> Christoph Freudenberger wrote:
> 
> > Do you have several 'GLU' residues in your protein and did you use
> > -sort -shuffle with grompp for the np4 job?
> >
> 
> I did not use -sort -shuffle with grompp.
> The difference in output actually arises due to small initial differences
> in forces (all initial coordinates and velocities are the same).
> The question is: How long schould be my MD simulations with different
> initial conditions in order to obtain the same average structures?
> 
> 
For a single molecule: very long, also dependent on temperature etc.

For many molecules: not long at all. Statistics converge with
sqrt(Nmol).


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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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