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

Berk Hess hess at kth.se
Thu Oct 17 13:45:01 CEST 2013


I would suggest to use the Buckingham functionalilty, set C6 to zero and 
modify lines 957-959 of src/mdlib/tables.c to fill the table with your 
potential instead of exp(-a*r).



On 10/17/2013 01:30 PM, Mark Abraham wrote:
> 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: ? Exp[-2A(r-r*)] -2 ?
>     Exp[-A(r-r*)]
>     So I have to define g® = ? Exp[-2A(r-r*)]  and h®=-2 ?
>     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%28s%29> 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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