Orientation colvar + metadynamics questions

From: Benjamin Bouvier (benjamin.bouvier_at_ibcp.fr)
Date: Thu Feb 21 2013 - 04:58:48 CST

Hello all,

I'm attempting to use quaternions (colvar 'orientation') as a biasing
coordinate for a metadynamics simulation, to control the orientation of a
molecule with respect to another. I have a few questions that neither the
documentation nor my first results have completely answered:

- Am I correct in assuming that the 'orientation' colvar is affected by
the overall rotation of the system, meaning that if I want to control the
orientation of B relative to A, I have to restrain the rotation of A
(using, e.g., another 'orientation' colvar and a 'harmonic' restraint)?

- How exactly is the width of the hill Gaussians (in R^4) defined from the
scalar 'width' parameter? I could find no trivial relationship between
this parameter and the width of the hills (also scalar) given in the
colvars.state file.

- Since 'orientation' is not grid-compatible, PMF output seems disabled.
Is there a utility program to convert the hills file to a PMF, or should I
write my own (which would require me to understand the aforementioned
hill-width thing...)?

Thanks for any info,

Benjamin Bouvier

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