[gmx-users] Crystal Surfaces in GROMACS

[Justin Lemkul]

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 
unit cell.

-Justin

> 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.
>
> -Tom
>
>> 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
>> Message-ID:
>>     <CAMJZ6qEQN8zqQQseAhkES=jxn-isDtDLn2LcgXvbWNfcFDKKuA at mail.gmail.com>
>> Content-Type: text/plain; charset="UTF-8"
>>
>> Hi,
>>
>> 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:
>>
>> https://pubs.rsc.org/en/content/articlehtml/2016/nr/c5nr07061a
>> https://pubs.acs.org/doi/abs/10.1021/acsnano.6b05274
>> https://pubs.acs.org/doi/abs/10.1021/acsnano.8b01692
>>
>> 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.
>>
>> Alex
>>
>> 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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>>
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>> End of gromacs.org_gmx-users Digest, Vol 174, Issue 87
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>
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
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