[gmx-users] change potential funtions

Erik Lindahl lindahl at csb.stanford.edu
Tue Feb 10 17:11:02 CET 2004

On Feb 10, 2004, at 4:44 PM, Nguyen Hoang Phuong wrote:

>>>> for some reasons I have to modify the proper dihedral angle 
>>>> potential
>>>> function and the van der Waals, electrostatic potential functions. 
>>>> The
>>>> modification is very simple: V_modify = kT*V_real where k the 
>>>> Boltzmann
>>>> constant and T temperature, V_real is the original potential and 
>>>> V_modify
>>>> is the one I would like to have. To make such change, could you 
>>>> please
>>>> tell me where is the right starting point and which is the 
>>>> subroutine I
>>>> need to change? Thank you very much in advance.
>> Please be more specific. The units for your function are now Energy^2,
>> since V_real is energy and kT is energy.
> thank David, the V_modify must be (kT/\hbar\omega)*V_real where
> \hbar\omega is known quantity.

Is T a constant temperature (i.e. given in the input file), or the 
actual temperature in the run?

If it does not change in the run, the easiest solution by far is to 
change the input parameters in the force field.

> The forces are calculate analytically or numerically?

They are calculated analytically, apart from the tabulated functions of 
course, where they are calculated from the table (you could probably 
call that semi-numerically, since it is not just a simple numerical 
derivation, but not quite analytical... see the manual for details).



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