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. > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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