[gmx-users] Re: Applying a Lennard-Jones Gauss potential function for TIP5P water

Justin Lemkul 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 -
> 2*(sig/r)^6]
> 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.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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