[gmx-users] Coulomb energies

Cesar Lopez inmuno_cl at yahoo.com
Sat Mar 19 18:49:14 CET 2005

Dear Gromacs users:

I used Gromacs to repeat a simulation of the method
LIE (Peter A. Kollman 1999 ) with the Trypsin and the

I have obtained similar values of binding free energy,
at least using LIE method and the clasical equation,
when I analyzed the punctual energies of my sistem (
drug in water and drug in protein) I saw that the LJ
energier are very similar to the Wan der vals
aproximation that they used, but when I compare the
Coulomb energies (In Gromacs  S-R Coulomb energies)
are very different, for example ,They had 114 Kcal/mol
in protein and 110 Kcal/mol in water, while I obtained
240 and 220 KJ/mol in each case.

My questions are:
Can different methods obtain different coulomb
Is there any difference If I use constraints????? or
maybe cutt-offs?
Is the forcefield the guilty?

The strange Is that I have repeated with more proteins
and the behavior is similar , differents coulomb
energies, similar LJ to the experiments, and the free
energy similar to the experimental.
Thanks for your time

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