[gmx-users] The free energy of vdw part

[Tanping Li]

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.