[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
regards
Reza
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