[gmx-users] Coulomb term calculation in gromacs

[Justin Lemkul]

On 11/22/19 11:08 AM, nikolaev at spbau.ru wrote:
> 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?

Electrostatics are calculated the same way everywhere (within the 
short-range cutoff), unless the force field applies a scaling factor to 
this interaction (fudgeQQ).

> 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?

Yes.

> 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?

Interactions within rlist (direct space) are computed by the normal 
(shifted) Coulomb potential.

> 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?

A diatomic molecule cannot have 1-4 interactions, unless you have added 
[pairs] for the 1-2 interaction, which mdrun will interpret as a 1-4 
interaction (because in that case, it's what you've told it to do). A 
pair interaction would be incorrect for a diatomic molecule.

-Justin

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Justin A. Lemkul, Ph.D.
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