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

[Johannes Kamp]

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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