Dear gmx users, I am calculating the free energy of solvating a small ligand by water, using FEP method. The free energy is separated into the contribution of electric+vdw. I find problem for the vdw part.
I am using gromacs-3.3.1. In the top file, I set the state B of ligand where LJ parameters of atoms are zero; in the mdp file, I set the lamda=0. According to my understanding, above setting should gives me the energy of ligand's state A. However, when I calculate the energy with a mdp with "free_energy=No" and a top without setting the B state, I get a very different energy. I tried but haven't dig out which part I missed. I greatly appreciate your help and consideration on this issue. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
