Re: FEP implementation in NAMD

From: Jérôme Hénin (jhenin_at_vitae.cmm.upenn.edu)
Date: Wed Aug 02 2006 - 21:16:17 CDT

Hi Naveen,

> 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.
That's correct, although some options are currently being tested, so future
versions of NAMD should have that feature.

> 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).
The scaling is not applied to charges or LJ coefficients, but directly to the
forces and energies.

> 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?)
No, within-group interactions are preserved. The scaling only affects
nonbonded interactions between one atom of the initial state and one atom of
the final state.

Best,
Jerome

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