[gmx-users] (no subject)

Jason Zhu jasonzhu925 at gmail.com
Fri Jul 14 02:41:28 CEST 2017

Dear Alex,

Many thanks for your replies and helping.

I totally agree with your comments about infinite molecules and periodic
boundary condition.

Here in our simulations, the hBN sheet covers the box dimensions (6nm*6nm)
without free edges. By using PBC and "periodic-molecules = yes", we could
calculate the surface energy of hBN sheet without effects of edges.

The parameters of force field we are using are borrowed from the following
papers. We introduced them into the Gromos force field. We are having a new
publication using this modified force field in which all the parameters are
shown explicitly. I could send it to you when it is published online. The
functions and parameters are fitted by the setting of "nrexcl=3" in these
papers. We couldn't make any changes for this. But we could try to use
larger value of "nrexcl" to fit the force field of hBN and include
short-range non-bonded interactions into bonded interactions. Thank you for
your suggestions.

1. Hilder, T. A. et al. Validity of current force fields for simulations on
boron nitride nanotubes. IET Micro & Nano Letters 5, 150-156,
doi:10.1049/mnl.2009.0112 (2010).

2. Kamath, G. & Baker, G. A. Are ionic liquids suitable media for boron
nitride exfoliation and dispersion? Insight via molecular dynamics. RSC
Advances 3, 8197-8202, doi:10.1039/c3ra40488a (2013).

3. Wu, J., Wang, B., Wei, Y., Yang, R. & Dresselhaus, M. Mechanics and
Mechanically Tunable Band Gap in Single-Layer Hexagonal Boron-Nitride.
Materials Research Letters 1, 200-206, doi:10.1080/21663831.2013.824516


Message: 5
Date: Wed, 12 Jul 2017 19:12:26 -0600
From: Alex <nedomacho at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Subject: Re: [gmx-users] Periodic Molecule's Free Energy Calculation
Message-ID: <4b927ef2-9a56-6655-8053-d284cf88b755 at gmail.com>
Content-Type: text/plain; charset=utf-8; format=flowed

> I wonder if the "couple-intramol = yes" is a must. Does it have any
> influence on the output results if we turn off the intra-molecular
> non-bonded interactions of a large infinite molecule?
The answer to your question has nothing to do with Gromacs, but with
understanding the difference between crystals and biomolecules (for
which Gromacs was designed).
Also (unrelated), it is a common misconception to believe that PBC makes
something infinite -- the effective size of your system is entirely
determined by the supercell size (proof: consider the ripples in hBN and
determine the lowest wavelength of the ripple that can propagate -- it
is commensurate with the box size). In an infinite system, you can have
an immensely long wave (though not infinite, as shown by Landau a while
back). PBC does not make anything infinite, it is a mathematical way of
avoiding surfaces.
> There is no universal force field for HBN, so I am using a modified
> gromos54a7_atb force field, i.e., manually adding the parameters for
> boron and nitrogen to the bonded & nonbonded .itp files.
Oh, I know that there is no force fields for these structures. ;) My
question was about which Gromacs ff you were using to insert your
parameters, and, most importantly, where those parameters came from.

> The parameters are obtained from literature.
What literature? All bio-style ff adaptations of solid-state potentials
(e.g. Tersoff-Brenner for hBN) I am aware of make it very clear that
"intramolecular" interactions between atoms sharing up to a fairly
distant covalently bound neighbor are limited to bonds and angles. This
comes from the math involved in developing potentials for crystals.
There was a recent question regarding this very problem here, which was
solved by setting a larger nrexcl value. In your case, you solved it
with turning off intramolecular coupling. In fact, if you set your
nrexcl to something like 4 or 5, you may not even need to turn off the
coupling. But then again, I don't know where the parameters came from.


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