Re: FixedAtoms and Reference group in spinangle colvar

From: nicolas martin (nicolasmartin973_at_gmail.com)
Date: Sun May 11 2014 - 16:52:42 CDT

Hi Jérôme,

Thank you for your answer. I tried to include in my refgroup selection the
hydrogens around C1 and C2. So the selection contains now 8 atoms. But
still, the result remains the same.

Do you think skipping this step assuming that it is due to the fact that
butane is not really what NAMD is made to work with and going to the next
step which is actual work on my protein would be a good idea? I mean how
can I make sure that I am not mistaken there and that it’s just a matter of
size and not because of me not fully understanding how to use that
powerful tool ?

Thank you again, bests,

NM

2014-05-09 20:53 GMT+02:00 Jérôme Hénin <jerome.henin_at_ibpc.fr>:

> 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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