[gmx-users] Re: positive Leonard Jones Energy (Mark Abraham)

Gideon Lapidoth glapidoth at gmail.com
Mon Sep 19 08:52:05 CEST 2011

Hi Mark,
Thanks for your answer. My ultimate goal is to compare biding affinities
between different ligands to the same protein using the LIE method. two
things bother though; First is the relatively high electrostatic  energy I
got between the ligand and the solvent which is considerably higher (about 5
times higher) than the electrostatic energy between the molecule and the
protein , therefore using the lie equation I got a positive delta G of
binding  which is obviously not correct (the LJ energy values cannot
compensate for the electrostatic energy difference). Secondly, my more
immediate concern is to understand why I would get a positive LJ value.

What do you think?


> Hi all,
> I ran g_energy in order to calculate the LJ energy between a pip2
> (Phosphatidylinositol 4,5-bisphosphate) molecule and the
> solvent using GROMACS 4.0.7. the pip2  molecule is very polar and the
> avg. coulomb energy value I got between the ligand and solvent was ~
> 3100 KJ.

An equilibrated condensed-phase system of mixed positive and negative
charges using a normal biomolecular force field should have negative
Coulomb PE.

> The solvent includes water molecules and Cl and Na ions to counter the
> pip2 charge. the production run was done in npt conditions. the total
> charge of the pip2 molecule is -6 e. The avg. LJ  energy I got was
> ~190 KJ.
> I am trying make sense of this. could it be that the polar
> interactions between the solvent and ligand are so strong that they
> can influence a positive LJ energy?
> Does anyone have any idea why this could be ?

Force fields are parameterized to reproduce certain experimental or
computational results, in the hope that such reproduction will permit
simulations using that force field to sample similar chemical ensembles
with correct frequencies. They're not parameterized such that the
absolute values of any energies or energy components means anything, and
one has to work hard to demonstrate anything sensible about energy
differences, too. What were you hoping to observe?



Gideon Lapidoth,

MS.c candidate

Hemi Gutman Biophysics Lab

Department of Biochemistry & Molecular Biology

George S. Wise Faculty of Life Sciences

Tel Aviv University

Israel 69978


Tel: (972-3) 640-9824
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