AMBER Archive (2003)

Subject: AMBER: RMSD and Radius of Gyration

From: Endres, Robert G. (endresrg_at_ornl.gov)
Date: Sat Oct 25 2003 - 17:24:07 CDT

Dear AMBER users,
what's the best way to calculate the radius of gyration (moment of inertia) with amber?

Also, comparing rmsd plots from Ptraj with the movie of same trajectory,
I cannot recognize very much correlation between between "good structures"
by inspection from movie and smallness of the rmsd value. Does anyone know how the fit to a reference structure in ptraj is done? This optimization procedure
seems to me highly nontrivial.

Thanks for any suggestions,

Best regards,
  Robert

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