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

Mark Abraham mark.j.abraham at gmail.com
Thu Oct 17 13:30:22 CEST 2013


It's hard to make any sense of the formatting of your equations, and you
haven't said what over what quantity your A varies or what r and r* are...
Do check out manual sections 4.2.13 and 6.9.


On Tue, Oct 15, 2013 at 10:02 PM, Reza Ghafarian Shirazi <
rezagh at student.uef.fi> wrote:

>  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<http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials#Constructing_the_Table(s)> 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.
>  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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