Multicopy simulations

[Lutz.Ehrlich@EMBL-Heidelberg.de]

Hi there,


maybe you could give me some feedback regarding multicopy simulations. I'd
like to run simulations as follows: Multiple copies of one molecule don't
interact with one another. Instead, they experience forces from interacting
with a single copy of another molecule. This other molecule feels the mean
of the force from the multiple copies.

I'm currently considering to implement this in NAMD, but I'd like to
prototype the thing in MMTK first. My first idea would be to create a
forcefield class that can handle the above interactions but then I wasn't
sure that the  molecular representation of MMTK would allow that. A first
attempt would be to create multiple collections of molecules and then let
those interact. The forcefield evaluator would then cope with the proper
scaling of the forces. But how could I keep multiple copies of regions of a
protein only (in the LocallyEnhancedSampling sense)? Just keep multiple
collections of those subregions and then evaluate forces with subsets that
look like 
	(singleMolecule1Collection, singleMolecule2RegionCollection +
		singleMolecule2subRegionCopy1Collection )
etc.? Hope you get what I mean...

Anyway I'm just at the very beginning. Is anybody out there working on such
a thing already? I'd appreciate any feedback.

Cheers,
	Lutz

______________________________________________________________________

Lutz Ehrlich		email:	lutz.ehrlich@embl-heidelberg.de
EMBL			web  :  http://www.embl-heidelberg.de/~ehrlich
Meyerhofstr. 1		
D-69012 Heidelberg	phone: +49-6221-387-140
Germany			fax  : +49-6221-387-517