Re: FixedAtoms and Reference group in spinangle colvar

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri May 09 2014 - 13:53:56 CDT

Hi Nicolas,

I think the most likely issue is that 3 atoms is not sufficient for the refPositionsGroup to be fitted properly. With this setup you should be able to make it a little larger.

Cheers,
J

----- Original Message -----
> 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
>
>
> spinangle.in :
>
> 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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