Simultaneous FEP simulation of two distinct residues

From: Christian Jorgensen (
Date: Tue Dec 14 2010 - 13:44:10 CST

Hi all,

In a normal free energy perturbation simulation, one selection/group is simulated for a creation/annihilation event that yields a free energy change deltaG.

If two residues are studied, currently two options exist:
I) Run two simulations, one for each residue, and obtain two free energy values deltaG(1) and deltaG(2)
II) Run one simulation and obtain an average over the two groups deltaG, where deltaG= (1/2)[deltaG(1) + deltaG(2)]. The disadvantage is that the free energy value is only an average value, not entirely representative of the two distinct residues.

I have a dipeptide Glu-GluP that I wish to study in a single simulation. I wish to create a proton in Glu and annihilate the proton in GluP.
I want to study this in a single simulation, but I do not want the average value over the two groups. I want to obtain the distinct values pertaining to the two groups studied deltaG(1) and deltaG(2)

My question: Is there a way of configuring the NAMD FEP configuration file and/or hybrid PDB file to study two distinct creation/annihilation processes during one simulation and obtain the free energy values for the two processes?

Thank you very much

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