FEP output in NAMD

From: Vani Krishna (vakri2002_at_yahoo.com)
Date: Tue Apr 05 2005 - 11:26:39 CDT


I have just started reading/understanding the free
energy perturbation method implemented in NAMD. I have
some questions:

(1) Can these calculations be done under NPT
conditions? or only NVT?

(2) I have a protein with two ligands L1, L2 and iam
attempting to compute the relative free energy of
binfing between these two ligands. For one of the
ligand I have the crystallographic positions and for
the other, i have taken the ligand coordinates after
5ns of MD simulation. if i did not turn on the
"minimize" option in the configuration file, i had
problems with RATTLE. So i turned it on for sometime
and then FEP resumed. Iam not sure if this is OK.

(3)From the manual, I understand that "dE_avg" is the
accumulated energy ensemble average and "dG" is
corresponding free energy at each step. What is this
"dG" that is calculated? to calculate average energy
for a particular window, the manual says "dE_avg"
should be summed. is this what goes into the final
equation to compute overall relative free energy of
sum(window_size*avergae_energy in that window)?

in that context, iam confused about "dG".


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