United Atoms in NAMD

From: Rajan Vatassery (r-vatassery_at_northwestern.edu)
Date: Fri Sep 29 2006 - 02:08:12 CDT

Dear List,
        I am just starting to use NAMD and I really would like to use it to
simulate a lipid-containing molecule in the same simulation as a
polypeptide. I think the lipid molecules in the simulation should not
need to be atomistic, and so I would like to approximate each -CH2-
group as a single particle (simple united atom approach).

        Searching the help files, and the previous questions posted here, as
well as the web and Web Of Science revealed that there's almost no work
done on (or even discussion about) NAMD with united atoms.

        Can someone explain this to me? Is it simply a matter of adapting the
UA approach to a NAMD-friendly parameter set? Has anyone tried UA with
NAMD? What problems would be encountered putting UAs in CHARMM? Thanks
in advance,


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