[gmx-developers] Defining an exponential functional form in tabulated potentials

Christoph Junghans junghans at votca.org
Fri Oct 18 16:56:53 CEST 2013

2013/10/15 Reza Ghafarian Shirazi <rezagh at student.uef.fi>:
> Dear all,
> I'm trying to define modified morse potential in Gromacs to be used as a
> forcefield using tabulated potentials.
> My potential's functional form is as: ε Exp[-2A(r-r*)] -2 ε Exp[-A(r-r*)]
> So I have to define g(R) = ε Exp[-2A(r-r*)]  and h(R)=-2 ε Exp[-A(r-r*)]. They
> have to be defined as values in a xvg table where the table is filled with
> values of r, f(R), f'(R), g(R),....
> My question is how can I make vales of these functions, while there's a
> variable in the exponential term.
> I saw in the manual on the website noting that h(R) for buckingham is
> expressed as h(R)=AExp[-Br] so I was wondering how they make the table of h(R)
> values while B is a variable.
Considering all atom type combinations, how many different values for
A,B do you have in your case?

> Solutions which cam ego my mind were:
> Should we use some mathematical approximations like Exp[-u]=1-u.
> or simply tabulated potentials does not support potentials more complex than
> lennard jones, and Buckingham is an integrated feature which doesn't need
> the xvv table.
> Any suggestions will be appreciated
> regards
> Reza
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Christoph Junghans
Web: http://www.compphys.de

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