[gmx-users] A question regarding electrostatic and coulomb energies.

[IÑIGO SAENZ]

Dear Mark,

I've been researching about energy groups and I think that it isn't the
solution for my problems.
The background of my question is the following:
I'm currently working with the people that develops ACEMD and because of
that I've got access to some information that ACEMD uses for its
calculations.
For each system that I simulate, I've got the list of all the pairs of
atoms that must be excluded in the nonbonded calculations (e.g. atoms that
are bound, 1-3 bound atoms and so on)
On the other hand, I also have a list of all the pairs that must be
included in the nonbonded calculations (1-n bound atoms, for n>=4 and so on)

The point is that I need to use that information (and more info that ACEMD
provides me) to generate a .gro and .top file in order to be able to run
the systems both in ACEMD and in Gromacs.

When I perform a SPE of a system in both ACEMD and Gromacs, the bond, angle
and dihedral energies are approximately equals in both, but Coulomb and VDW
energies are very very different and this is driving me crazy.

Hoping that you can help me, if any of you need more information about the
.gro, the .top or the information that ACEMD provides me, don't hesitate in
contact me.

Thank you very much in advance.

Iñigo S.