AMBER Archive (2001)

Subject: Re: trajectory analysis

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Jul 24 2001 - 13:48:54 CDT

        I have two questions that I hope someone can enlighten me on:
        1. Is it possible to perform an AMBER simulation while taking out the
        rigid body motion? (Subtracting angular momentum perdiodically)

See NTCM and NSCM.

        2. Is it possible to take out rigid body motion from an AMBER
        trajectory?
        
This can be done by rms-fitting the coordinates to a static model.
Carnal and probably ptraj can do this. (Carnal uses a mass-weighted
fit, while ptraj may use a simple geometrical fit.)

Bill Ross