[gmx-users] Crystal Surfaces in GROMACS

Alex nedomacho at gmail.com
Wed Oct 31 23:24:20 CET 2018


There are two main reasons there aren't any serious tutorials: first,
Gromacs wasn't originally intended for this type of simulations and second,
it's not clear what such a tutorial would describe. If you have a suitable
interaction model for the material you'd like to simulate, the "usual"
rules (box dimensions commensurate with PBC for a given crystal structure,
careful relaxation procedures, thermostat/barostat considerations, etc) of
solid-state simulations apply, i.e. there isn't anything terribly specific
to representing any such systems in Gromacs, given that it remains a very
well designed general MD tool to work with non-reactive systems. We've used
Gromacs to simulate 2D materials in aqueous environment, maybe they could
be helpful:


For polymers, it would similarly hinge on the existence of a forcefield and
if it doesn't exist, well, you will have to develop it. ;) If the processes
of interest involve reactive forcefields (i.e. covalent bonds get broken
and created), then you need another MD package, e.g., LAMMPS.

Hope this helps.


On Wed, Oct 31, 2018 at 2:42 PM tca1 <tca1 at rice.edu> wrote:

> I've been trying to find out if there are any tutorials on simulating
> crystals (specifically crystal surfaces) using GROMACS; most of the
> tutorials I can find online seem to focus on finite-sized biomolecules
> and I don't know how the topology and run parameters would change with
> periodic surfaces.
> For context, I'm interested in studying some aspects of polymer
> behavior at solvent-surface interfaces, and a 2D crytalline surface
> seems like the most direct way to model this, but if there's a
> different way of representing such interfaces in GROMACS, I'd also be
> interested in pursuing that approach.
> Thanks,
> Thomas Allen
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