[gmx-users] Treating electrostatics and van der Waals interactions differently

[Mark Abraham]

On Fri, Mar 15, 2013 at 7:27 PM, Jeff Woodford <
jwoodford at missouriwestern.edu> wrote:

> Hi all,
> I am attempting to simulate a system that has strong ionic character so I
> would like to treat the electrostatics and van der Waals interactions
> separately.  For example I would like to include all pairs of atoms in the
> electrostatics calculation but I would like to exclude 1-2 and 1-3
> neighbors in the van der Waals calculation.  Is this possible to do in
> GROMACS?  If so, how might this be accomplished?  Thanks in advance for
> your help.
>

Should be possible, but I don't think it's something for which GROMACS
explicitly caters. I'd suggest keeping the normal exclusions for the
[moleculetype] (e.g. nrexcl=3). For each 1-2 and 1-3 interaction, add
[pairs] interactions that have zero VDW parameters. See manual 5.3.4, and
other bits of chapter 5. You may be able to hijack the [pairtypes]
mechanism here, depending whether the [pairs] mechanism is already being
used by your force field for 1-4 interactions. Otherwise, I think something
like

[pairs]
; i j functype c6 c12
1 3 1 0 0

is the right kind of way to put a no-LJ normal-Coulomb interaction between
atoms 1 and 3. Not sure offhand how to scale down the charges (which you'd
probably want).

You'd have to generate that list of 1-2 and 1-3 pairs yourself, but you can
probably hijack the contents of the [bonds] and [angles] fields to save
some legwork.

Mark