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

Reza Ghafarian Shirazi rezagh at student.uef.fi
Tue Oct 15 22:02:59 CEST 2013

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® = ε Exp[-2A(r-r*)]  and h®=-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®, f'®, g®,….
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<http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials#Constructing_the_Table(s)> noting that h® for buckingham is expressed as h®=AExp[-Br] so I was wondering how they make the table of h® values while B is a variable.

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

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