[gmx-users] Re: Some questions on Tabulated Dihedral Potential

[Ran Friedman]

Hi Johannes,

Thanks for the correction - you're right of course (when deltaX = 1 it's
the same).

To be closer to the gromacs code it's
der = (y[N+1] - y[N-1]) * 0.5 * tabscale

where
tabscale = number of points per nm (or degree for angles/dihedrals).

Ran.

Johannes Kamp wrote:
> Hi Ran,
>
> are you sure the derivative is calculated as:
> der = (y[N+1] - y[N-1]) * 0.5 * deltaX
>
> and not as:
> der = (y[N+1] - y[N-1]) * 0.5 / deltaX ?
>
> The last calculation makes a little more sense to me...
>
> -Johannes
>
>
>>> Ran Friedman wrote:
>>>> Hi,
>>>>
>>>> The numerical derivative for the Nth value y[N] is calculated as:
>>>> der = y[N+1] - y[N-1] * 0.5 * deltaX
>>> Correction:
>>> der = (y[N+1] - y[N-1]) * 0.5 * deltaX
>>>> where y is the potential deltaX is the difference between two
>>>> successive values in your input (e.g., 1 if you have a table that
>>>> goes from -180 to 180 with 361 values).
>>>>
>>>> I don't think you can print the number without changing the code,
>>>> but it's not difficult to calculate. You can plot your forces and
>>>> -der and see where they deviate.
>>>>
>>>> Ran.
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