[gmx-users] Crystal Simulation

tca1 tca1 at rice.edu
Fri Nov 2 23:19:26 CET 2018

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  


> 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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