[gmx-users] Extract of free energy difference from FEP

[bmbbl at leeds.ac.uk]

Dear all,

I used FEP protocol indicated in mail list before to obtain two .edr files from
normal (A) and perturbed (B) simulations. But g_energy really confuses me.

1. g_energy -f A.edr -f2 B.edr -fee -o -ravg
 Should I select potential energy term or total energy?
2.g_energy -f B.edr -f2 A.edr -fee -o -ravg
 I can extract dV/dlamda. Should I use this term or potential energy term?
3. What can I do with ravg.xvg?

Thanks for any advice.

Best,
Binbin