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 <nedoma...@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 <nedoma...@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 <nedoma...@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 > >>>> -- > >>>> Gromacs Users mailing list > >>>> > >>>> * Please search the archive at > >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>>> posting! > >>>> > >>>> * Can't post? 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