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
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
