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

[Barrett Worley]

Ah, I had to go into one of this paper's references to find the units I
needed, then I was able to convert units properly.

Thanks for leading me to that, Andre.

Now, I just have to figure out why K for bond angles is reported in units
of dyn/cm (which converts to kJ/mol*nm^2) by N. Wakabayashi, but GROMACS
requires kJ/mol*rad^2.



On Thu, May 19, 2016 at 9:18 AM, André Farias de Moura <moura at ufscar.br>
wrote:

> 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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>
>
> --
> _____________
>
> Prof. Dr. André Farias de Moura
> Department of Chemistry
> Federal University of São Carlos
> São Carlos - Brazil
> phone: +55-16-3351-8090
> --
> Gromacs Users mailing list
>
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-- 
Barrett Worley
Doctoral Candidate
Dodabalapur Group
Dept. of Chemistry
The University of Texas at Austin