From: Cheri McFerrin (cmcfer1_at_lsu.edu)
Date: Sat May 19 2007 - 08:11:57 CDT
hi all,
i am interested in running a NAMD simulation using o-ter-phenyl (2
phenyl rings attached to a benzene at its ortho positions) as this
molecule goes through a glass-transition temperature when the
temperature is gradually lowered. i would like to represent
o-ter-phenyl as 3 points in space with a rigid bond distance
between these points, each point has zero charge, and the angle
between the 3 points is approx 72 degrees. does anyone know how to
run a NAMD simulation when the bond distances and angles are
constrained to constant values?
thanks in advance. cheri mcferrin
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