[gmx-users] errors depending on (lack of) solvent
spoel at xray.bmc.uu.se
Tue Jan 27 17:21:04 CET 2004
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?
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
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