[gmx-users] partial exclusion of interactions within 1-4
mark.j.abraham at gmail.com
Tue May 22 09:48:33 CEST 2018
What does the documentation of nrexcl in the reference manual say?
On Tue, May 22, 2018, 08:51 Alex <nedomacho at gmail.com> wrote:
> Okay, let me try to rephrase the question, because it seems that I am
> definitely unable to make it work and noone's replied so far.
> I have a "molecule" (a periodic boron nitride sheet) and a stand-alone
> itp file for it -- everything works, i.e. it's a stable, well-behaved
> structure the way I set it up.
> Within that molecule (and nowhere else) I need Coulombic interactions
> between closest neighbors, while all other non-bonded interactions
> should obey an effective nrexcl = 3. Is this something that can be done
> in Gromacs?
> Thank you.
> On 5/16/2018 7:12 PM, Alex wrote:
> > Hi all,
> > I think I understand how it works, but to double-check... There's a
> > paper describing a setup of intramolecular interactions for boron
> > nitride (https://pubs.acs.org/doi/10.1021/acs.jpclett.7b03443), in
> > which non-bonded interactions *within* 1-4 were set up in the
> > following way: LJ is off, but all electrostatic interactions are on.
> > This is to achieve a better representation of the phonon spectrum and
> > in fact it appears physically correct.
> > Does this mean setting nrexcl to 1 for the crystal topology and
> > creating a table of nonbond_param between B and N with sigma and
> > epsilon equal to 0?
> > Thanks,
> > Alex
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