**From:** Philip Fowler (*p.w.fowler_at_qmul.ac.uk*)

**Date:** Mon Jan 10 2005 - 11:12:41 CST

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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?

Thanks,

--Phil

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

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