FEP calculation of dimerization

From: Christopher Hartshorn (cmhartshorn_at_wsu.edu)
Date: Sun Nov 16 2008 - 23:45:05 CST

Hello all. I have a few questions about NAMD's abilty to run the FEP

First, can the free energy of dimerization between two molecules be
calculated? And if so, would one make a hybrid structure that
included the two monomers, separated in space, and the dimer
(somewhere in the middle)? Or by some other method?

Second, this is probably an obvious question but I felt I should ask
before wasting CPU time, when I add the fep portion to my config. file
(e.g. turn on the free energy perturbation), will all of the other
values (e.g temps, bonded/nonbonded energies, pressures, etc.) still
be output? In other words, does turning on the fep simply add another
value that is output? And if so, does this increase cpu time
drastically or not at all?

Thank you.

Christopher M Hartshorn

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