NAMD Carbohydrate Simulations

From: Niels Johan Christensen (njc_at_kvl.dk)
Date: Fri Nov 09 2007 - 06:39:10 CST

Dear NAMDers.

Obviously a lot of work on large biomolecular systems has been carried
out with great success using NAMD, and indeed the lions share of
publications citing NAMD concerns simulations of systems of such large
dimensions. I was wondering if anyone have had the opportunity to
thoroughly explore the simulation of solvated 'small' biomolecules using
NAMD. To be more specific: I wish to perform hydration studies of
disaccharides (e.g. cellobiose) employing the the forcefield CSFF (M.
Kuttel, J. W. Brady and K. J. Naidoo, /J. Computational Chemistry/,
23(13),1236-1243 (2002)) in NAMD. I can see no theoretical objections to
this idea, however I find the conspicuous lack of NAMD studies on
similar systems slightly unsettling. For some reason, researchers seem
to prefer the AMBER or CHARMm programs for such studies.

Any suggestions or advices are highly appreciated.

Best regards
Niels
 

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