Re: [AMBER] restraining mean square displacements

From: Adrian Roitberg <>
Date: Fri, 5 Aug 2016 15:54:33 -0400

Mean square displacement tells you about how FAR you are from some
target. B-Factors report on Mean Square fluctuations, which are HOW MUCH
you fluctuate around some average. RMSD and RMSF are two very different


On 8/5/16 3:52 PM, Irem Altan wrote:
> Hi,
> In the manual, the following is said about restraints:
> “Restraints can also be defined in terms of the root-mean-square coordinate distance from some reference structure. This allows one to bias trajectories either towards or away from some target.”
> How does this work exactly? Would this function allow for the protein atoms to have mean square displacements that are compatible with the B-factors reported in the PDB file?
> Best,
> Irem
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Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
AMBER mailing list
Received on Fri Aug 05 2016 - 13:00:03 PDT
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