Subject: Re: parallel md+mc

From: Guido Germano <[email-masked]>
Date: Sat, 12 Sep 1998 14:28:19 -0400 (EDT)

Sorry, but you don't need to start your MD run from an *equilibrated*
configuration. You can use MD itself to reach equilibrium. So the
question should be: from which configuration start? There are two main
possibilities: construct a regular crystal-like arrangement and melt it
rising the temperature, or construct a random arrangement at lower
density and compress it gradually during the first steps of the run.
The first approach is easier and good enough for your case.

May I be so cheeky to question the scientific interest of your project?
The challenges in MD nowadays are molecular materials with bonded and
long range (Coulomb) interactions. There are a number of general-purpose
parallel programs around (have a look at http://antas.agraria.uniss.it
for a fairly comprehensive list), but none shows completely satisfying
speedups. Getting good speedups for LJ fluids is trivial. A better use
of T3E time is e.g. proteins: I think that's why there are no papers
about O(10^6) LJ particles in the literature, even if they have been
technically possible since some years. Of course I am glad to hear your
or anybody else's counterarguments on this opinion of mine.

Regards

Dr. Guido Germano

Research Assistant in Theoretical Physics, University of Bristol, England
Tel. +44-117-928 9000 ext. 8755, http://www.phy.bris.ac.uk/staff/germano_g.html

On Wed, 9 Sep 1998, Matthias Hloucha wrote:

> Keywords: massive parallel computing (Cray T3E, MPI), molecular dynamics,
> monte carlo, lennard-jones mixture
> 
> Dear colleagues,
> 
> at the Central Institute for Applied Mathematics (ZAM), Juelich, Germany,
> we started a project to investigate massive parallel algorithms for
> molecular dynamic simulations. We want to simulate very many (O(10^6))
> simple (LJ) particles.
> 
> One important task is to construct an equilibrated start configuration
> before starting the md runs. Do you think it is resonable to use Monte
> Carlo techniques to equilibrate very many simple particles? Are you aware
> of any existing code in this area?
> 
> Thank you very much for your kind consideration,
> 
> Best wishes,
> 
> Matthias