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

From: Ajasja Ljubetič (
Date: Thu Feb 09 2012 - 12:05:19 CST

Dear Jrme and Giacomo,

Yes, you can use these two variables to find out the difference between
> colvars and VMD fitting. However, I don't suppose there is an issue with
> the vector distance between the two centers of geometry, right? :-)
No, no, but this data is still needed to align the two structures.

The function in the tcl file attached (sorry, I forgot to upload it in the
> VMD script library some time ago) prints you the rotation matrix that you
> can use with "atomselect moveby" in VMD. It is a 4x4 matrix as per VMD's
> format.

No problem, I managed to find a wrong formula for the conversion at (Q54). This is why I had
some problems. I should have just listened to wikipedia
PS: It's just "atomselect move".

My guess is that if you have a well-defined structure (read: thermal
> fluctuations are much smaller than the radius of gyration of the reference
> coordinates), the colvars' matrix and that computed by VMD via the Kabsch
> method should be pretty much the same. If you're not in those conditions,
> they may differ, but in that case they are both not very meaningful.
The RMSD as given from the colvars or calculated in VMD is exactly the same
(when using the correct weight as you pointed out). (shown
So hopefully all my configuration files are OK.

Using a more defined structure is very good advice. So when I use the whole
backbone as a reference I obtain the correct
PMF<> as
opposed to what I had
when using just the backbone atoms and the CB atom of the spin label.

Taking a closer look at the orientation colvar in both cases (in terms of
the rotation angle and the unit vector of rotation) was also very
educational (shown
for me. Basically I expected that the five backbone atoms determine the
orientation quite well, but this obviously is not the case. Perhaps if one
would use a moving average of the atom positions the situation would

Anyway I'm just happy that the PMFs obtained
and without <> are
the same. So the neglected derivatives of the optimal rotation don't appear
to cause any problems.

Thank you and best regards,

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