[gmx-users] Crystal Simulation

Thu Nov 1 22:18:28 CET 2018

In that case it sounds like gmx x2top is what I need, but reading  
about it online suggests I also need some kind of residue entry for  
the crystal itself. I'm not clear what this entry needs to include in  
order to work properly with x2top for a periodic crystal, so do you  
have some specific .rtp and .top files I could look at for an example  
system to see how  you set this up?

Thanks,
Tom

> Message: 1
> Date: Wed, 31 Oct 2018 18:25:34 -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] gromacs.org_gmx-users Digest, Vol 174, Issue
> 	87
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> 	<CAMJZ6qF2oSiuJVe8KsCma3Ntovk_WHq8hLBhKn2jiPQTe8nNxw at mail.gmail.com>
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> The connectivity is set at the topology creation stage, which is separate
> from the mdp option "periodic-molecules."  As long as the box size is
> commensurate with the crystal and the edges are properly periodic, gmx
> x2top used with proper options will create connectivity across the box
> without any trouble. We use it routinely on crystal structures and it works
> fine.
>
> Alex
>
> On Wed, Oct 31, 2018 at 5:46 PM tca1 <tca1 at rice.edu> 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?
>>
>> 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. 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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