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
objects.
adrian
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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Aug 05 2016 - 13:00:03 PDT
