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

[André Farias de Moura]

Hi Barret,

authors of that paper state which units they are using for energy, distance
and angles - all other units might be inferred from units reasoning. For
your specific concern, kb must have units of eV/Ų in their tables of
parameters, leading to kJ/mol/nm² in the GROMACS convention after proper
conversions are applied.

If you're not 100% sure about that, you may either contact the authors of
that paper or check the original references from where they have taken
these parameters.

best,

Andre

On Wed, May 18, 2016 at 6:45 PM, Barrett Worley <bcworley at utexas.edu> wrote:

> 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
> --
> Gromacs Users mailing list
>
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> posting!
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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