FixedAtoms and Reference group in spinangle colvar

From: nicolas martin (
Date: Fri May 09 2014 - 09:01:28 CDT

Dear NAMD users,

I ask for your help once more concerning my issues with spinangle.
I'm working on butane (I know this is not ideal due to the fact that it's a
small molecule that could create problems for fittings) and I'm trying to
use spinangle covlar to compute a PMF along the rotation of the dihedral
angle defined by C1 C2 C3 and C4. This is done on purpose because I plan to
move on a protein so the obviously solution of using a dihedral colvar
isn't my first choice. C1 C2 and C3 are included into the reference group
and if I'm right this allows me to cancel any rotation or translation
effects to THEN compute the spinangle with contains as well a fitting
between a reference structure a the current one (superimposed with the
atoms specified in refgroup as said before).

I tried first the following colvar defnition and in addition used the
keyword fixedAtoms to fix C1 C2 and C3 and I got a nice match between this
PMF and the one obtained with a simple dihedral colvar (my reference).

Then I removed the fixedAtoms keyword and here is my problem, my PMF is not
anymore what I expected.

So please tell me where is my mistake? I thought it would be the same and I
wouldn't need to fix any atoms since I'm fitting C1 C2 and C3 to the
reference structure...?

And if I move on my protein, how can I then make sure than the diffusion
(even if it shoul be really less than butane's diffusion) isn't introducing
a bias in my PMF?

Thanks a lot in advance for your help ,

NM :

colvarsTrajFrequency 1

colvar {
        name spinangle
        spinangle {
                axis (-1.408,-0.537,-0.317) # axis of bond C2 C3

                atoms {
                        atomNumbers 8 9 10 11 #..moving group
                        centerReference on
                        rotateReference on
                        refPositionsGroup { #..reference group
                                atomNumbers 1 5 8
                        refPositionsFile ../input/buta.pdb
                refPositionsFile ../input/buta.pdb

harmonic {
        name harmonic
        colvars spinangle
        forceConstant 0.006
        centers XXXX

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