Issues with 'Gyration' in Colvars module

From: Jérôme Hénin (
Date: Fri May 25 2012 - 13:20:49 CDT

[re-sending in clipped form to avoid mailer issues]

Hi Shaon,

As Giacomo noted, there is a discrepancy between what's implemented
and what is documented - this probably escaped us because our typical
test cases have atoms with identical masses. That may well be the
cause of your problem, because the Jacobian used for the ABF
implementation is definitely that of the unweighted function. For this
kind of variable, the Jacobian correction always yields a biasing
force that pushes toward small values, and increases as 1/Rg.

Did you include hydrogen atoms in your definition of Rg? That would
make it more sensitive to this issue.

In any case, the code calculating this should be changed. We have a
fix in the works: the mass weighting will become optional to
accommodate all cases. In the meantime, I am attaching a source file
that disables it, if that's any help.


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