Re: NAMD question

From: Peter Freddolino (
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

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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