[gmx-users] Crystal Simulation

[Alex]

You're most welcome. Unfortunately, I do not have an answer for your
question. I assume you've used x2top on a properly sized system, in which
case all bonds and angles across the box should be created properly. The
issues with domain decomposition may be due to the box being far from
cubic. I think others here may be able to help with this better than me.

Alex

On Fri, Nov 2, 2018 at 4:19 PM tca1 <tca1 at rice.edu> wrote:

> Thanks for explaining the format, I'm now able to successfully
> generate a topology file with periodic bonds in place. However, when I
> try to minimize the structure, I get an error stating that:
>
> "Not all bonded interactions have been properly assigned to the domain
> decomposition cells"
>
> I also see some lines in the log file pointing out that with
> periodic-molecules on, the domain decomposition isn't sure what
> baseline size to use for the cells. Does this error have something to
> do with additional setup I need to do for a periodic crystal structure
> like this, or is something else more likely? I'm only running a very
> simple minimization, steepest descents over a few thousand atoms as a
> test.
>
> -Tom
>
> > Message: 1
> > Date: Thu, 1 Nov 2018 15:55:09 -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 Simulation
> > Message-ID:
> >       <
> CAMJZ6qGC6Qfht1bRUuqGupvY5cSom9a1TQb8QMM6fxMmdpoLxA at mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > 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
> >
>
>
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