[gmx-users] Parameterization of OPLS-AA force field for MoS2 simulation in GROMACS.

André Farias de Moura moura at ufscar.br
Wed May 18 23:29:38 CEST 2016

Hi Barret,

It looks like you just have to make the proper conversion of units (eV to
kJ/mol and angstrom to nm), but Lennard-Jones seems to be a little tricky,
since the authors defined different S-S interactions for atom in the same
plane or in different planes (not an issue if you are planning single-sheet



On Wed, May 18, 2016 at 6:12 PM, Barrett Worley <bcworley at utexas.edu> wrote:

> Hello all,
> I'm trying to modify the OPLS-AA force field parameters for Mo and S atoms
> to simulate monolayer MoS2. I'm following the general procedure suggested
> here: http://chembytes.wikidot.com/grocnt
> <
> http://www.linkedin.com/redir/redirect?url=http%3A%2F%2Fchembytes%2Ewikidot%2Ecom%2Fgrocnt&urlhash=VkOA&_t=tracking_anet
> >,
> but they use existing OPLS-AA values for atomtypes, bondtypes, etc. To my
> knowledge, there is no Mo atom in OPLS-AA standard force fields.
> I've read the Varshney paper "MD simulations of molybdenum disulphide
> (MoS2): Force-field parameterization and thermal transport behavior," and
> would like to use the parameters listed there in my force field. However,
> I'm having difficulty translating their parameters for set 9 into relevant
> GROMACS .itp parameters.
> For example, how would one translate bond coefficients K and r0 to
> bondtypes values b0 and kb? Or am I even on the right track?
> Any help on this matter would be greatly appreciated!
> Thanks,
> Barrett
> --
> Barrett Worley
> Doctoral Candidate
> Dodabalapur Group
> Dept. of Chemistry
> The University of Texas at Austin
> --
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Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090

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