FEP simulations?

From: Christopher Hartshorn (cmhartshorn_at_wsu.edu)
Date: Tue Nov 18 2008 - 13:19:13 CST

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

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 very much for any time involved in replying to this.

Christopher M Hartshorn
WSU
cmhartshorn_at_wsu.edu

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