AMBER Archive (2004)

Subject: AMBER: Removal of rotation: Flying ice cube

From: koby levy (
Date: Tue May 18 2004 - 19:23:54 CDT

Dear Amber users,

I am simulating a system (using sander classic, Amber6) where part of the
system is fixed (by setting very large mass for these atoms). I chose this
way to freeze atoms (instead of ibelly) to be able to remove rotational
motion. However, I notice that in most of the trajectories my system is
trapped and the flexible region freely rotates while the protein is almost
frozen. This is probably what was observed previously for DNA simulations
(using Amber) as "The flying ice cube".
In these simulations I apply the removal of rotation and translation
by the NSCM. Does the NSCM work? Is a special treatment required to get
rid of the rotation motion in such cases?

thank you in advance for any suggestion,
Koby Levy

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