[EMAIL PROTECTED] wrote:
Haven't looked into the details yet, but this is worth noting for those
interested. Thanks William.
----- Forwarded message from [EMAIL PROTECTED] -----
Date: Sat, 01 Sep 2007 00:15:25 -0400
From: William Noid <[EMAIL PROTECTED]>
Reply-To: William Noid <[EMAIL PROTECTED]>
Subject: what is the force function for proper dihedrals
To: [EMAIL PROTECTED]
howdy,
i am guessing that you want a formula for the cartesian force on the
atoms involved in a 4-body bonded interaction that is parameterized by a
dihedral angle. if so then all you have to do (of course) is to work
out a sort of nasty jacobian transforming the coordinates, but of course
it is kind of messy/cumbersome and easy to make a mistake. the only
published place i know where they have the answer explicitly is in the
dl_poly manual, which you can find at
http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/. they work it out in
gory detail on page 18 of the manual (which is actually page 30 of the
pdf file). i can't promise there are no typos there, but i think it is
quite likely correct. i have explicitly checked their calculation for
valence angles, though this is considerably easier. but at least this
would give you something to check against. one warning in advance: the
dl_poly folks define vectors in the opposite convention from normal.
see in the figure that r_ij is the vector from i to j - whereas i would
have defined r_ij as the vector from j to i.
anyway, i hope this is helpful. if this is what you wanted maybe you
could forward the info to the mailing list. if not, sorry to cause you
any bother.
there is a conference proceedings specifying how gromacs does it, which
is slightly more efficient than computing derivatives straight away.
looking at the title I get slightly uncertain. I have the book in my
office will have a look next week.
@inproceedings{Bekker93b,
author = {H. Bekker and H. J. C. Berendsen and E. J. Dijkstra
and S. Achterop and R. v. Drunen and D. v. d. Spoel and A. Sij\-bers and
H. Keegstra and B. Reitsma and M. K. R. Renardus},
title = {Gromacs Method of Virial Calculation Using a Single Sum},
booktitle = {Physics Computing 92},
pages = {257--261},
year = {1993},
editor = {R. A. de Groot and J. Nadrchal},
address = {Singapore},
publisher = {World Scientific},
}
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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