[gmx-users] Fwd: what is the force function for proper dihedrals

[chris.neale at utoronto.ca]

Haven't looked into the details yet, but this is worth noting for  
those interested. Thanks William.

----- Forwarded message from wnoid at hec.utah.edu -----
     Date: Sat, 01 Sep 2007 00:15:25 -0400
     From: William Noid <wnoid at hec.utah.edu>
Reply-To: William Noid <wnoid at hec.utah.edu>
  Subject: what is the force function for proper dihedrals
       To: chris.neale at utoronto.ca

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.


peace,


will noid


----- End forwarded message -----