[gmx-users] RE: Monte Carlo in Gromacs for the Future

David van der Spoel spoel at xray.bmc.uu.se
Thu Aug 19 08:46:45 CEST 2004

> > 
> >> On Wed, 2004-08-18 , David van der Spoel wrote:
> >> It is not very high priority for the developers, but it wouldn't be very hard either. Erik L. has implemented a version >> of the inner loops that does not compute forces, and hence would be even faster for MC. What is needed is that someone >> writes an integration algorithm. If someone is interested to do it please let us know...
> Is it possible to have a copy of what Dr. Erik Lindahl has already written. I'm not sure we will be able to finish anything interesting, but we can look at it. Is what Erik got meant to stand as a MC module by itself or can it already be hybridized with MD?
> Can you please be more specific about what you mean by integration algorithm? Do you mean the mc moves?
It is not really necessary to have the newest changes as they will
merely make the calculations faster. 

To implement MC what would need to be done is to add another alogrithm
(like in src/kernel/md.c routine do_md). You would have to replace that
subroutine by a new one, or rather add a new one, e.g. do_mc. Here you
should implement mc moves, including preferential moves if you so wish.
The do_md routine just calls the gromacs routines that compute energies
(and for now, forces too, but that will change by adding or modifying a
single flag). If you feel like doing this, and have further questions
then we should probably move this thread to the developers list.

David van der Spoel, PhD, Assoc. 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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