(no subject)

From: Debaditya Mukherjee (debadityam7_at_gmail.com)
Date: Wed Mar 08 2017 - 22:52:17 CST

Hi all NAMD users,

I performed alchemical FEP (both forward and backward) of a hybrid
structure of DJ-1, containing both alanine and threonine (A2T) at position
104. After running the simulations for 1ns, the total free energy change
(forward) = 0.63, and for (backward) = 0.60, when i tried to generate the
total free energy(overall) using the VMD FEP SIMULATION ANALYZER, the total
free energy change came as 0.3, whereas it should have been around 0.6. Can
someone please help me out how to analyze this result, and where has it
gone wrong.

Debaditya Mukherjee,
M.Sc. Biotechnology (final year),
VIT University, Vellore

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