[gmx-users] positive Leonard Jones Energy

Gideon Lapidoth glapidoth at gmail.com
Sun Sep 18 17:13:48 CEST 2011

Hi all,

I ran g_energy in order to calculate the LJ energy between a pip2
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. 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 ?

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