On 1/14/14, 8:07 AM, 李晴 wrote:
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?
No.
http://gromacs.5086.x6.nabble.com/What-is-epsilon-r-td4888079.html
What makes you believe the van der Waals and Coulombic interactions should be
equal in terms of energy? If there is some experimental reason for that
statement, then the results simply suggest that your parametrization of the
ligand is incorrect.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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