[gmx-users] Crystal Simulation

Thu Nov 1 23:03:36 CET 2018

Here is an example for bulk molybdenum disulfide. These directives go into
atomname2type.n2t in your forcefield directory (I usually have a
stand-alone directory in the local simulation folder):

MO  opls_2000   0.5   95.940  6  S 0.237 S 0.237 S 0.237 S 0.237 S 0.237 S
0.237 ;bulk MO
S   opls_2004  -0.25  32.065  3  MO 0.237 MO 0.237 MO 0.237
     ;bulk S

The concept is very simple: the leftmost entry is the label, then the opls
type you've given it throughout the forcefield, then charge, then mass,
then the number of bonds it participates in, then the list of constituents
in those bonds with corresponding distances. x2top uses those distances
with a 10% tolerance to set types in the corresponding topologies.

In other words, MO atom has a type opls_2000, a charge of +0.5, a mass of
such and such, has a total of six nearest neighbors of the type S, each
residing at the distance of 0.237 nm. Those neighbors can all be different
with different bond lengths, etc. The only thing left to do after this is
set up your bonded and nonbonded parameters for these types and off you go.
Note that the charge and the mass present in the atomname2type will
override the values on ffnonbonded.itp. Definitely the case for the charge
(I never really had different masses set in the two directives). Hope this
helps.

Alex

On Thu, Nov 1, 2018 at 3:18 PM tca1 <tca1 at rice.edu> wrote:

> 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
> > Message-ID:
> >       <
> CAMJZ6qF2oSiuJVe8KsCma3Ntovk_WHq8hLBhKn2jiPQTe8nNxw at mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > 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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