Re: "Goodness" of Trajectory

From: Michael Cooney <>
Date: Thu 18 Jan 2001 14:29:25 -0500 (EST)


There are various ways to check the quality of a trajectory, but
the most quickly informative is probably to calculate the RMS deviations
for a selected set of atoms, e.g. protein backbone, all heavy atoms, etc.
This RMSD figure normally rises during the first 10 to 50 ps (or more) of
a simulation, depending on the size of the system, but then should
stabilize for the rest of the calculation. You can also monitor torsions,
distances, or bond angles. Carnal is the program in Amber that calculates
RMSD, distances, etc. It's in the Amber manuals, or I can send a sample
input. Good luck!

Best regards,

Michael Cooney
Dept. of Biochemistry and Molecular Biology
The University of Georgia
Athens, GA 30602

On Tue, 16 Jan 2001, Troy Bothwell wrote:

> I was curious as to what veteran users of amber do to evaluate the goodness
> of their simulation. Obviously junk in, junk out, but do you periodically
> test with some standard or other mechanism.
> Thanks for your responses,
> Troy Bothwell
Received on Thu Jan 18 2001 - 11:29:25 PST
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