thermodynamic integration and NAMD: soft-core or "separation-shifted" vdw potentials

From: Philip Fowler (
Date: Mon Jan 10 2005 - 11:12:41 CST

Hi everyone,

I have already run one calculation of a difference in binding free energy
using the FEP module within NAMD. I am about to start calculating a second
and need your help .

In my first calculation (and this will happen again) I encountered the
well-known "end-point catastrophe" where, because the van der Waals component
is scaled linearly by lambda, the repulsive term remains and prevents the
water exploring the void created when the atom has truly vanished.

One solution to this is to follow the "separation-shifted" method of
Zacharias, Straatsma & McCammon (J Chem Phys 100 9025 (1994)) where, for
nonbonded interactions with alchemicalk atoms, the conventional vdW LJ form

V = (1-lambda) [ A/r^12 - B/r^6 ]

is replaced by

V = (1-lambda) [ A/(r^2 +dlambda)^6 - B/(r^2 +dlambda)^3 ]

(where dlambda is a supplied parameter)

which is the same when lambda = 1. This form allows a much smoother transition
as lambda=0,1 is approached.

Now the questions are,

1) how and where would one change this in the source code? I have had a
rummage but understanding the object structure would take me more time than I
would like (I am not an expert at C++). In principal the logic is simple: for
alchemical nonbonded vdw interactions, apply the new functional form, for
everything else, keep it as it is.

2) would this be useful to anyone else?



Philip Fowler, 
PhD Student
Centre for Computational Science,
UCL Chemistry

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