[gmx-users] Periodic Molecule's Free Energy Calculation Error

Alex nedomacho at gmail.com
Fri Jul 14 08:44:24 CEST 2017

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!


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 <nedomacho at gmail.com <mailto:nedomacho at gmail.com>>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org>>
> Subject: Re: [gmx-users] Periodic Molecule's Free Energy Calculation
>         Error
> Message-ID: <4b927ef2-9a56-6655-8053-d284cf88b755 at gmail.com 
> <mailto:4b927ef2-9a56-6655-8053-d284cf88b755 at 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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