[gmx-users] The free energy of vdw part
jia_11_osu at yahoo.com
Thu Feb 16 17:28:08 CET 2012
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.
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