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

[Reza Ghafarian Shirazi]

Thanks for your reply,

It's hard to make any sense of the formatting of your equations

it's the standard morse equation used in many references<http://lammps.sandia.gov/doc/pair_morse.html>. the buckingham and Lennard jones have a very high degree of deviation and using them makes no sense for my application.
I'm defining potentials using ab-initio calculations and at high levels of theory and large basis sets and I need a good potential function.

and you haven't said what over what quantity your A varies or what r and r* are

r* is a parameter calculated using fitting, r is the radius, A and should be defined as coefficients of g® and h®, and since I dunno how to define and exponential term I can not define them. This is the problem.

Hi,

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.

Mark


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