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

[David]

On Mon, 2004-01-26 at 18:13, gianluca santarossa wrote:
> 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?

You can run with MPI, but without shake, or set 
constraints = h-bonds
it's probably not worthwhile though.

> 
> > 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
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++