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

[Mark Abraham]

Hi,

That's what we hope people use the tables of contents and text searches for
;-) Next year's reference manual content will come also on the web, so
Google will search it, but the feature to beam exactly what you want
directly into your brain is a few years away... :-D

The reference manual has a subsection "5.4.3 Intramolecular pair
interactions" which is cross referenced from the big tables 5.4 and 5.5
that briefly describe all the directives and link into the supporting text.

Mark

On Wed, May 23, 2018 at 11:14 AM Alex <nedomacho at gmail.com> wrote:

> This is the part I don't really understand, as I've never done this
> before. Let's assume we generated those pairs (it would actually be easy
> to obtain directly from bonds/angles/dihedrals). LJ is set throughout
> the system. Can one specify pairs with specific LJ params only for those
> pairs? In other words, will the [pairs] section accept columns like 'i j
> sigma epsilon'?
>
> Feel free to tell me to RTFM, I just wish it could come with an
> _approximate_ page number... :)
>
> Thanks,
>
> Alex
>
>
> On 5/23/2018 2:59 AM, Mark Abraham wrote:
> > 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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