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

[gianluca santarossa]

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?

Tanks
gianluca

-- 

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