question about setting up FEP calculations

From: Shyno Mathew (
Date: Mon Oct 14 2013 - 10:48:46 CDT

Dear all,
I am doing FEP calculations. For my system, I am mutating more than 1
residue at the same time (all are same type of mutations). Since this is my
first time doing free energy calculations, I am trying to set up the system
as mentioned in the tutorial:
"A tutorial to set up alchemical free energy perturbation calculations in
As the first step, I am writing the .fep input file which contains all toms

(appearing, disappearing and non-changing atoms). Initially, I was doing
FEP immediately after minimization. However it wasn't running. So I did a
short run (about 3 ns) after minimization. Then submitted FEP runs, this
worked. I would like to confirm this approach is correct.

When I did the short run (3 ns), the system has both disappearing and
appearing atoms. For eg. the hydrogen attached to a carbon atom will
disappear and a methyl group will appear. In my system I have both hydrogen
and methyl atom bonded to the carbon atom at the same time during the 3 ns
run. Is this approach correct?
Any help will be appreciated,

Shyno Mathew
PhD student
Department of Chemical Engineering
Columbia University

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