Sure - one should use a tool capable of doing the job, and use its optional
capabilities accordingly. Choosing non-bonded exclusions based on bonds, in
a way that does not implement the intended model physics, is indeed wrong,
but that doesn't make the use of modified 1-4 pair interactions "childish"
in general ;-)
You are correct. My point only holds in a situation where people indeed
are doing that: using an inappropriate tool. And you see how many people
on this list ask questions about doing solid-state simulations with
Gromacs. I have a dual background and could give many examples where the
use of what works for proteins/lipids in water is, well, childish, for
lack of a better word in solid-state systems. I hope noone takes
offense. :) The "problem" is that, thanks to your hard work, Gromacs is
delightful to use, much more so than LAMMPS, and my hope is that one day
you guys will just implement things like REBO and ReaxFF and MEAM, and
Weber-Stillinger and what-not. If you do that, I will fly to your
location, give you a hug, and personally buy you a steak dinner. In
other words, my hope is that one day Gromacs will be an appropriate tool
for all of classical MD, solid or liquid state.
So, for the record, the actual issue is that GROMACS does not implement
some kind of tapering of non-bonded interactions that would apply between
particle pairs at short range?
Within the question initially posed (about silica), Gromacs is fairly
capable of everything necessary, it is just a matter of carefully
reading the documentation on the original solid-state potential and then
setting up the adopted forcefield, including the nrexl, etc. The much
bigger issue (with solid-state things in general) is the springs for
bonds, angles, etc, and use permanent molecular topologies. Wrong phonon
spectra, wrong elastic properties away from 0K, wrong rippling spectra
of graphene and likely all atomically thin membranes, inability to do
covalent bond breaking/formation, etc, etc. That is, things Gromacs was
never intended for. But then again, see what I said above.
Alex
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