Hi Jason,
I didn't have time to look at all of those papers, but look for instance
at eq. (2) in Hilder et al's paper and the definition of the f_dmp
function on the right -- this tapers off short-range interactions for
close neighbors. I am not sure if this particular function results in
any serious difference (I think, given the value of R_r, it was designed
pretty much exactly to remove all nonbonded interactions closer than
second neighbor), but the point is that Gromacs doesn't use anything
like this. As a result, many things cannot be translated into Gromacs
FFs "as is," requiring a fairly broad range of effort from mild
tinkering all the way to complete reparameterization.. Even then the
best one can hope for with Gromacs when applied to the actual properties
of crystals is structure stability and correct bond lengths -- nothing
beyond that. This is really more of a general comment, because more and
more people are trying to simulate solid-state structures with Gromacs.
Best of luck!
Alex
On 7/13/2017 6:43 PM, Jason Zhu wrote:
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 (2013).
Best,
Jason
Message: 5
Date: Wed, 12 Jul 2017 19:12:26 -0600
From: Alex <nedoma...@gmail.com <mailto:nedoma...@gmail.com>>
To: Discussion list for GROMACS users <gmx-us...@gromacs.org
<mailto:gmx-us...@gromacs.org>>
Subject: Re: [gmx-users] Periodic Molecule's Free Energy Calculation
Error
Message-ID: <4b927ef2-9a56-6655-8053-d284cf88b...@gmail.com
<mailto:4b927ef2-9a56-6655-8053-d284cf88b...@gmail.com>>
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>
> 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.
Alex
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