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
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