[gmx-users] errors depending on (lack of) solvent

gianluca santarossa gianluca.santarossa at unimib.it
Mon Jan 26 18:15:01 CET 2004

On Mon, 2004-01-26 at 16:58, Erik Lindahl wrote:
> >
> > So, isn't there a way to run parallel simulations of a single molecule
> > on 2 or more machines?
> >
> Yes, it's possible if you don't constrain all bonds. It's pretty common 
> in the literature to constrain only bonds with hydrogens for this very 
> reason.
Sorry, but I didn't undersand. Is there a way to split a simulation of a
single molecule on, for istance, 4 machines, without using MPI?

> We might implement a parallel constraint solver, but I doubt it will be 
> useful apart from testing stuff since it will involve extra 
> communication (reducing performance).
My simulations consist of dynamics of quite small molecules ( 100 or 200
residues )  for a long time. Do you think that parallel computation
would be unuseful in my case?



Gianluca Santarossa
Molecular Modelling Laboratory
Dept. of Biothecnology and Biosciences
Universty of Milano Bicocca
P.zza della Scienza 2
20126 Milan, Italy
Tel: +39-02-6448-3475
gianluca.santarossa at unimib.it

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