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

[Barrett Worley]

Thanks for your reply, Andre.

I get that I need to convert units. According to the GROMACS manual, kb
units are kJ/mol*nm^2. However, the paper lists K in eV and the
equation for harmonic bonds and angles: K×(r-r0)^2, which would give me
eV*Å^2 (which I then convert Å to nm). These two sets of units are
incommensurate, yes?



On Wed, May 18, 2016 at 4:29 PM, André Farias de Moura <moura at ufscar.br>
wrote:

> 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
> models).
>
> best
>
> Andre
>
> 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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-- 
Barrett Worley
Doctoral Candidate
Dodabalapur Group
Dept. of Chemistry
The University of Texas at Austin