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. > > hong bingbing wrote: >> Hi, Ran, >> >> The potential f(x) and force -f'(x) in the table are calculated by >> myself before constructing the table. The potential can be written in >> an analytical form and the force is calculated as the analytical >> negative derivative of the potential at point x. There should not be >> so large deviation betw. the value I supplied and the value >> calculated by GROMACS. Wait. Is there something wrong in my >> interpretation? What's your method to get the force? Is there a way >> to see the numerical derivative generated by GROMACS? >> >> Thanks >> CH > > ------------------------------------------------------------------------ > > _______________________________________________ > 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
-- ------------------------------------------------------ Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355559 Email: r.fried...@bioc.unizh.ch Skype: ran.friedman ------------------------------------------------------
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