AMBER: RMSD and Radius of Gyration

From: Endres, Robert G. <>
Date: Sat, 25 Oct 2003 18:24:07 -0400

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,

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Mon Oct 27 2003 - 07:53:02 PST
Custom Search