[gmx-users] How much should epsilon-r be set?

李晴 sunny_lq at 163.com
Tue Jan 14 14:23:18 CET 2014

Dear gmx-users,
I use GMX to simulate a protein 700 peptide long with a ligand. The protein-ligand complex is put in a box with explicit water. I use AMBER99 force field.
The epsilon-r was set with the default value 1, with coulombtype=PME. The problem is, the energy generated from .xtc file using g_energy showed large difference between coulomb energy and VDW potential energy. For example, I calculate the energy between the ligand and the protein, which were, Coul-SR=-406.172, LJ-SR=-115.504. We thought during the protein-ligand interaction, the coulomb energy and VDW energy should have similar values. But the results seemed to indicate that coulomb force had a much more important impact on the interaction. 
Is there any problem I set the epsilon-r=1? Should I change it larger to weaken the coulomb impact?
The ligand locates in the active pocket of the protein, which is a hydrophilic environment and will attract several water molecules during MD.
Thanks a lot!

Qing Li

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