From: Matthew Davies (m.davies_at_mail.cryst.bbk.ac.uk)
Date: Wed Sep 19 2007 - 06:45:05 CDT
I have a question regarding the application of an ABF simulation.
In the ABF application of NAMD, the average force along the reaction
co-ordinate xi is
F(xi) = -dA(xi)/dxi = - <dV(x)/dxi> + 2RT/xi
The latter term in the repulsive force is due to the greater availability
of phase space as xi increases.
The question is whether, in the integration of the above to give A(xi),
the term 2RT/xi is removed in NAMD-ABF so that A(xi) tends to a constant
as xi -> infinity. Otherwise A(xi) -> minus infinity as the resulting 2RT
ln(xi) -> infinity (entropy increasing indefinitely) as xi -> infinity, .
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