[gmx-users] Free energy calculation

[bmbbl at leeds.ac.uk]

Dear all,
I use FEP perturbation method to work out the free energy difference of binding
ion to the membrane protein.

At the final step, I use g_energy -f ab.edr -f2 ab-perturb.edr -fee -o FE.xvg.
I find that the result is different from g_energy -f ab-perturb.edr -f2 ab.edr
-fee -o FE1.xvg

My first question is if I should use non-perturbed .edr as -f or -f2

When I use perturbed .edr as -f, there is a choice of dVpot/dlambda in g_energy
list. My second question is if I should select this value or the pure potential
energy?

Thanks for any advice.
Binbin