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> To: Discussion list for GROMACS users <gmx-us...@gromacs.org> Subject: Re: [gmx-users] Periodic Molecule's Free Energy Calculation Error Message-ID: <4b927ef2-9a56-6655-8053-d284cf88b...@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. Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.