[gmx-users] Coulomb term calculation in gromacs

[nikolaev at spbau.ru]

Dear Justin,

Thank you very much for your answer. I have a few more questions.


1)

>>
>> 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).
>

So, within the short-range cutoff all interactions between non-bonded
atoms are calculated with the Coulomb formula with f = 138.935.., am I
correct? I.e. the interactions between 1-4 atoms are calculated in the
same way? Why does .psf file include the "pairs" list for the 1-4 atom
pairs?

2)

>> 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 apply the Cut-off scheme, how is the electrostatics calculated beyond
the cut-off?

3)

>
>> 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.
>

So, does it mean that in case of PME scheme only the electrostatics beyond
the cutoff is calculated with PME formulae?



Best regards,
Dmitrii