From: Thomas Albers (talbers_at_binghamton.edu)
Date: Thu Jul 18 2013 - 11:21:30 CDT
Hello!
> Hello Thomas, the bias is only on the overall rotation, not on the internal
> degrees of freedom: any force applied to the orientation colvar doesn't have
> a projection along vectors that would change the internal structure of the
> protein.
Yes, but aren't the forces that are applied through the harmonic
restrains acting only on the backbone?
OK, one can argue that the random forces that cause the protein to
diffuse away from its original orientation act only on the exterior,
and the force applied to the backbone is of the same order of
magnitude.
I'm just slightly concerned that the colvar applies forces only to the
backbone, and that might introduce systematic error.
Regards,
Thomas
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