Dear LAMMPS users,
In order to estimate the free hydration energy of an ion (Na+) through the Thermodynamic Integration Method, I made use of the trajectories obtained at the full interaction potential (lambda=1) as the reference state, and successively changing the coupling parameter to 0.0, traced the ion-water interaction potential. The original system was made charge-neutral by insertion of a chloride anion into bulk water. The perturbation was accomplished by applying the soft pair potential and using the rerun command. It seems that the same approach is adopted by the “compute fep” command where the atom coordinates remain unchanged during such perturbation.
However, the reviewers of my paper have suggested that different series of simulations need to be conducted at each lambda value. I’m not sure if that is the right approach, because when the snapshots are not identical, it is not meaningful to compare the changes in the potential energy. On the other hand, at lambda values other than 1.0, my system won’t be charge-neutral any more. Could you please let me know about your opinion on this matter?
Many thanks in advance.