[gmx-users] Crystal Surfaces in GROMACS
jalemkul at vt.edu
Thu Nov 1 01:20:51 CET 2018
On 10/31/18 6:55 PM, tca1 wrote:
> The forces and parameters aren't a problem, that's all been developed
> separately. My main concern is the connectivity of the crystal surface
> itself with periodic images. Is there a way to explicitly denote a
> connection between atoms in the box and their periodic images, or do I
> just have to play with the box sizes and hope for the best?
The box needs to be correct, but if it is, then you can use gmx x2top
with the -pbc option to get a topology with bonds written to image atoms.
> I did see something about the periodic-molecules option while
> searching through the manual and online for this topic, but I can't
> find much detail about proper usage or if it's even relevant to what
> I'm working with here.
You will likely need it. If you have a bond between two atoms on
opposite "sides" of the central unit cell, then the periodic-molecules
option instructs mdrun to compute the bond between these two as the
minimum image distance rather than the bond length within the central
> Really any clarification on how to properly represent simple 2D
> crystal structures in simulations with GROMACS would be a great help;
> maybe this is covered in the papers you linked or associated SI, I can
> take a look there first.
>> Message: 3
>> Date: Wed, 31 Oct 2018 16:24:01 -0600
>> From: Alex <nedomacho at gmail.com>
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Cc: Discussion list for GROMACS users
>> <gromacs.org_gmx-users at maillist.sys.kth.se>
>> Subject: Re: [gmx-users] Crystal Surfaces in GROMACS
>> <CAMJZ6qEQN8zqQQseAhkES=jxn-isDtDLn2LcgXvbWNfcFDKKuA at mail.gmail.com>
>> Content-Type: text/plain; charset="UTF-8"
>> There are two main reasons there aren't any serious tutorials: first,
>> Gromacs wasn't originally intended for this type of simulations and
>> it's not clear what such a tutorial would describe. If you have a
>> interaction model for the material you'd like to simulate, the "usual"
>> rules (box dimensions commensurate with PBC for a given crystal
>> careful relaxation procedures, thermostat/barostat considerations,
>> etc) of
>> solid-state simulations apply, i.e. there isn't anything terribly
>> to representing any such systems in Gromacs, given that it remains a
>> well designed general MD tool to work with non-reactive systems.
>> We've used
>> Gromacs to simulate 2D materials in aqueous environment, maybe they
>> 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
>> 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.
>>> Thomas Allen
>>> Gromacs Users mailing list
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>> End of gromacs.org_gmx-users Digest, Vol 174, Issue 87
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
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