FEP implementation in NAMD

From: nmichaud_at_jhu.edu
Date: Wed Aug 02 2006 - 18:17:53 CDT

Hello group,

I am currently trying to implement the dual-topology method in LAMMPS
(another parallel MD code) and was wondering how the method is implemented
in NAMD (or if there is a reference that would be terrific). Does NAMD
currently use a soft-core approach to avoid the end-point catastrophe? I
found an email from last year stating that it doesn't, and nothing in the
current documentation or tutorial stating otherwise, so I assume not. Does
NAMD take the approach that Charmm takes, applying a correction to the
potential postpriori? Or is the potential modified before the beginning of
the simulation (say, applying the lambda scaling directly to the charges
and lennard jones coefficients of each group). Also, are within group
interactions scaled as well (ie, say you mutate an alanine to a lysine -
does the terminal amine group interact with lysine beta carbon at the
scaled level or normal level?) Thanks for any help.

Naveen Michaud-Agrawal

Naveen Michaud-Agrawal
Program in Molecular Biophysics
Johns Hopkins University
(410) 614 4435

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