[gmx-users] g_energy -fee -f2

[Xavier Periole]

One changes the topology according to the perturbation and generate a
new file.tpr and rerun. That what I would do. But I guess that if you change
the number of atoms (I don't know about the type though) the trajectory
will no longer correspond to the topology defined in the tpr and the program
will complain.
At that point I think somebody with the experience of FEP calculation
within gromacs would be of better use than my comments.

XAvier