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

[Christoph Freudenberger]

David van der Spoel wrote:
>>Is it enough about 100 ps or it schould be about 1000 ps,
>>for example, for protein with ~500 residues and ~4000 atoms, 300 K ?
> 
> It's a difficult question for which no good answer exists. At moderate
> temperature it can take very long (microseconds or more) to sample all
> conformations...
> 
But this is the general problem of MD, isn't it?
You never (really) know, when you have simulated long enough...
A trajectory of 1ns will be as good (or bad) if comes from
1 node or from 4 nodes.

As far as I understood it, this was the initial questions:
Which of the two trajectories is the "correct" one?

regards
-- 
Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785