From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sat May 19 2007 - 09:40:43 CDT
Hi Cheri,
it sounds like you're essentially looking for rigid body MD;
unfortunately NAMD doesn't yet do this (although it may sometime in the
future). The best you can do for now is use relatively stiff bonds and
angles.
Peter
Cheri McFerrin wrote:
>
> 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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