Re: Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module

From: Ajasja Ljubetič (
Date: Mon Feb 06 2012 - 16:55:26 CST

To answer part of my own question

> Is the colvars module using the same algorithm for molecule alignment as
> VMD?
The colvar module uses quaternations for finding the optimal rotation. So I
can define an orientation colvar and a DistanceVec colvar to obtain the
full transformation matrix, which would enable me to visualise exactly what
is going on using VMD.

By the way, where can the script " quaternion2rmatrix.tcl" be found?

Best regards,

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