Re: United Atoms in NAMD

From: Mark Abraham (
Date: Fri Sep 29 2006 - 02:26:36 CDT

Rajan Vatassery wrote:
> 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,

Molecular mechanics force fields can't be mixed and matched without
destroying what validity they have as physical models. "Putting UAs in
CHARMM" is thus a recipe for disaster. There's likely nothing intrinsic
about NAMD (or any other simulation program) that uses force fields read
from files to prevent some UA force field being invented, tested,
possibly converted from some other file format and/or finally deployed
in production calculations.

The most sensible approach is to find a force field that uses united
atoms that has been tested and shown to be useful for systems similar to
the one you want to study. That investigation will normally tell you
what MD/MC software those people used and it will be simplest to use
that. Otherwise, you can convert their force field into a format NAMD
reads and use NAMD.

In summary, choose your force field before your MD code, not the other
way around.


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