Re: Orientation colvar + metadynamics questions

From: Benjamin Bouvier (
Date: Thu Feb 21 2013 - 07:37:06 CST

Thanks for the answers Jérôme. One last question, if I may - in quaternion
space, is the biasing Gaussian function 'isotropic' (ie, same width
applied to all 4 dimensions), or are the scalar and vector parts treated
Best, Benjamin

On Thu, 21 Feb 2013 13:53:28 +0100, Jérôme Hénin <>

> Hi Benjamin,
> ----- Original Message -----
>> 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)?
> You are correct that the 'orientation' colvar is, in general, sensitive
> to overall rotations of the system, but incorrect in concluding that you
> need restraints. As with all colvars, you can define this orientation
> based on rotated coordinates, in the frame of reference of group A. to
> that effect, use the rotateReference and refPositionsGroup keywords,
> providing group A as the the refPositionsGroup.
>> - 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.
> The width of each Gaussian is considered to be twice its standard
> deviation, and it is obtained as the hillWidth parameter of
> metadynamics, times that colvar's width parameter. So the std. dev. is:
> 1/2 * hillWidth * colvar->width
>> - 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...)?
> I don't think there is such a utility at this point, but I hope the info
> above is enough for you to compute the PMF.
> Best,
> Jerome

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:22:58 CST