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

Alex nedomacho at gmail.com
Tue May 22 09:56:43 CEST 2018

I feel like I am being tested, but it says what I thought I knew: 
"defines the name of your molecule in this *.top and nrexcl = 3 stands 
for excluding non-bonded interactions between atoms that are no further 
than 3 bonds away."

This to me suggests that all coulombic+LJ interactions will be removed 
for neighbors closer than third. By setting nrexcl = 1, one would get 
nearest-neighbor coulombic back, along with LJ. However, I still want 
the LJ off. Does this make sense?


On 5/22/2018 1:48 AM, Mark Abraham wrote:
> Hi,
> What does the documentation of nrexcl in the reference manual say?
> Mark
> 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.
>> Alex
>> 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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