[gmx-users] partial exclusion of interactions within 1-4

Alex nedomacho at gmail.com
Tue May 22 08:51:19 CEST 2018

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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