[gmx-users] Re: Applying a Lennard-Jones Gauss potential function for TIP5P water
jalemkul at vt.edu
Thu Apr 18 20:28:11 CEST 2013
On 4/18/13 8:44 AM, Andrish Reddy wrote:
> Thanks Justin,
> I had a look at the manual regarding tabulated potentials... for clarity,
> The table values must contain: x, f(x), −f(x), g(x), −g(x), h(x), −h(x).
> For my function then would f(x) = 1/r g(x) = eps*[(sig/r)^12 -
> and h(x) = -epsG*[exp-(((r-rG)^2) / (2*sigG^2))] ?
> Also from the manual:
> "The parameters A, B, and C are read from the topology. The type of
> interaction, Lennard-Jones or Buckingham, is determined by the nbfunc
> parameter in the [ defaults ] directive of the topology."
> How would the A,B & C terms be applied to my function with 5 constants? What
> would 'nbfunc' have to be set to?
Sorry, I have no experience with complex cases like this. Set up a small test
case that can be easily verified and try your luck. Tabulated potentials are
definitely the way to go though, unless you want to completely overhaul the
Gromacs code to implement the new potential equation expression :)
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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