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

[Barrett Worley]

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