[gmx-users] Anybody using Silica InterfaceFF on Gromacs?

Alex nedomacho at gmail.com
Mon Jul 3 02:27:09 CEST 2017

> 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.


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