Regarding Delta Delta G in FEP calculation

From: snoze pa (snoze.pa_at_gmail.com)
Date: Thu Sep 20 2012 - 13:09:57 CDT

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Dear NAMD users,

 I was following the NAMD tutorials on Fep calculations but unable to get
the idea of calculating Delta Delat G, as shown in figure 8 of the FEP NAMD
manual. Base on this tutorial, there are four calculations in water
(Forward on, Forward off, backward on, backward off) and two in vacuum
(forward and backward).

So how should I calculate the delta delta G?

Delta Delta G = Delta G(forward on, water) - Delta G( forward, Vacuum)

or

Delta Delta G = Delta G(forward off, water) - Delta G( forward, Vacuum)

or

Delta Delta G = Delta G(backward on, water) - Delta G( backward, Vacuum)

or

Delta Delta G = Delta G(backward off, water) - Delta G( backward, Vacuum)

Where on or off means alchDecouple is on or off.

Thank you very much for your time and help.

S

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