[gmx-users] Coulomb term calculation in gromacs

[nikolaev at spbau.ru]

Dear all,

I have a question about the calculation of the Coulomb term in Gromacs.
As I understand, two terms are involved: Coulomb 1-4, which is calculated
among the 1st and 4th atoms, and the term for the rest of the
interactions.

In the manual the standard Coulomb formula is given with f = 138.935...,
is it applied for the Coulomb 1-4 interactions?

If I use the electrostatic scheme Cut-off, then the usual Coulomb formula
is applied for all atoms within the cutoff, excluding the 1-2, 1-3 and 1-4
bonded atoms?

If I use the PME scheme, then interactions between all atoms within the
rlist is calculated, excluding the 1-2, 1-3 and 1-4 bonded atoms, by
applying the Ewald sum?

Also, I have generated a model system of H2 molecule for gromacs and put
charges on both atoms, calculated the energy terms. However, the Coulomb
1-4 was not zero. How could that be? Was that related to the PBC & PME is
used?

Best regards,
Dmitrii