As I wrote it der is the derivative itself, so you should plot (-1)*der. Ran.
hong bingbing wrote: > Thanks Ran. Should there also be a minus sign before (y[N+1]-y[N-1]) > because the third column in the table is -f'(x)? > CH > > > > > > ------------------------------------------------------------------------ > *发件人:* Ran Friedman <r.fried...@bioc.uzh.ch> > *收件人:* Discussion list for GROMACS users <gmx-users@gromacs.org> > *已发送:* 2009/7/21(周二), 上午9:41:42 > *主题:* Re: 回复: [gmx-users] Re: Some questions on Tabulated > Dihedral Potential > > 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 =聽 (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 聽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 > ------------------------------------------------------ > > > ------------------------------------------------------------------------ > 好玩贺卡等你发,邮箱贺卡全新上线! > <http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/> > > ------------------------------------------------------------------------ > > _______________________________________________ > 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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