Re: question about setting up FEP calculations

From: Jérôme Hénin (
Date: Mon Oct 14 2013 - 14:32:34 CDT

Hi Shyno,

There seems to be something wrong with your approach. If you do an equilibration run prior to the FEP, you should do that at a well-defined lambda state, by enabling the alchemical options and setting lambada to either 0 or 1, depending on where you want to start from.


----- Original Message -----
> 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,
> thanks,
> Shyno
> --
> Shyno Mathew
> PhD student
> Department of Chemical Engineering
> Columbia University

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