[gmx-users] positive Leonard Jones Energy

[Mark Abraham]

On 19/09/2011 1:13 AM, Gideon Lapidoth wrote:
> 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?

Mark
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