NAMD question

From: Cheri McFerrin (cmcfer1_at_lsu.edu)
Date: Sat May 19 2007 - 08:11:57 CDT

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  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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