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

[Mark Abraham]

Hi,

I suggested that [pairs] with the LJ parameters specified as zero was a way
to be non-simultaneous. That adds back the Coulomb you want.

Mark

On Wed, May 23, 2018 at 10:55 AM Alex <nedomacho at gmail.com> wrote:

> It is my understanding that either [pairs] or [exclusions] affect LJ and
> electrostatics simultaneously, please correct me if I'm wrong. Maybe
> this just isn't meant to be, being a highly artificial setup
> (nearest-neighbor electrostatics on, LJ off)... The idea for this comes
> from authors who used LAMMPS, and that thing allows such tricks with ease.
>
> The setup is almost guaranteed to work for me without including these
> interactions (just set nrexcl=3 and go home), but I am needlessly
> hesitating. In addition, I am absolutely against LAMMPS in this
> particular case -- my postdoc is using it heavily on the same machine
> with the same GPUs and it's massively slower (I estimate 5-7 times for
> identical system size) than Gromacs. I just can't have 20-30 ns as my
> simulated time.
>
> Alex
>
>
> On 5/22/2018 3:17 AM, Mark Abraham wrote:
> > Hi,
> >
> > That sounds right, given the wording (which I just didn't remember right
> > then). So now that we understand that nrexcl applies to all moleculetypes
> > in the .top then we pick whichever of 1 or 3 is most convenient (probably
> > 1) and add either manual [pairs] or manual [exclusions] to the
> appropriate
> > moleculetypes until it works how we want. In particular, the manual
> [pairs]
> > should be able to have LJ parameters specified that are zero when you
> want
> > that. nrexcl and fudge values are just sugar for common cases of these
> > patterns.
> >
> > Mark
> >
> > On Tue, May 22, 2018, 09:57 Alex <nedomacho at gmail.com> wrote:
> >
> >> 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?
> >>
> >> Alex
> >>
> >>
> >> 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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