Molecular dynamics for interpolation?

Mark Israel userisra at mts.ucs.ualberta.ca
Wed Nov 27 17:17:48 EST 1991


   I am trying to make a video of a protein unfolding.  What I have to
work from is "snapshot" coordinate sets ("artist's conceptions") of the
protein in various stages of unfolding.  I would like to interpolate
between these snapshots in a biochemically realistic fashion.  (Previously
I tried interpolating "naively" with splines, but the motion was not
convincing.)

   Therefore I have been doing molecular dynamics with Axel Br"unger's
X-PLOR package.  I can get from one snapshot to the next all right, 
but I can't get there in a smooth fashion.  The RMS shift between one
output frame and the next varies wildly; it depends generally on the
harmonic term, but it's too erratic for me to control it.

   Can anyone point me to alternative software -- a molecular dynamics
package with which I *could* restrain the RMS shift?

   Any suggestions would be appreciated.

					Mark Israel
I have heard the Wobble!		userisra at mts.ucs.ualberta.ca




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