[gmx-users] errors depending on (lack of) solvent
feenstra at chem.vu.nl
Wed Jan 28 09:09:16 CET 2004
gianluca santarossa wrote:
> 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?
No, communication between CPU's is done via MPI, always. But, the limitation
is in solving (distance) constraints (e.g., for constant bondlengths).
> 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?
If it is in vacuum, you can get to 100's of ns's in a week or so on a
single CPU. I don't see what you might gain by adding a few factors
in speed to that. If you have (explicit) water, you have many more
molecules and you can go up to 8-16 CPU's (depending on the amoount
of water, and the type of machine you have and the hard- and software
setup of it).
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" |
| | (Red Hot Chili Peppers) |
More information about the gromacs.org_gmx-users