From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu May 22 2014 - 07:00:25 CDT
This could be linked to the precise geometry of your problem. The dihedral angle is measured after projection on a plane orthogonal to the middle vector (groups 2 and 3), so that should be oriented exactly as the axis for spinAngle.
Translational fitting should not affect this, only rotations would matter.
I didn't get the attachment, can you send it off-list?
----- Original Message -----
> Dear all, drear Giacomo,
> As you advised me, I decided to move on with a new molecule, ethyl-benzene.
> Same as before concerning my purpose. I define here the rotation axis for
> the spinangle as the bond between the atom on the ring and the next to it
> which is the first of the ethyl moiety. So I compute the free energy of the
> rotation of the final carbon (my selection is actually final carbon the one
> before and the 2 H on it) of the ethyl group around the bound defined
> beforehand. I must admit that I have no more fitting problems in VMD so I
> guess no more in the refgroup fitting if they are both using the same
> But I came up with a new problem. I can observe a shift on the PMF (see
> file attached) between both methods I used, dihedral and spinangle. If I'm
> right, the way I set everything should lead me to the same profile. But I'm
> concerned with one detail. Since the center of geometry of my selection to
> compute the spinangle (the last part of my ethyl moeity) is not exactly on
> the axis defined beforehand, the axis will be first shifted to go through
> this center of geometry and might this somehow interact with the rotation
> energy ? I have checked the applied forces and can't get anything relevant
> for my problem out of it. Any ideas?
> Thanks a lot for you help
> 2014-05-12 0:27 GMT+02:00 Giacomo Fiorin <giacomo.fiorin_at_gmail.com>:
> > Hello Nicolas, as I mentioned earlier and Jérôme pointed out as well,
> > butane is a very small and flexible molecule, not suitable for defining a
> > rigid-body rotation. Including the hydrogens won't help, because they are
> > even more flexible than the carbon atoms, in particular the methyl
> > hydrogens which can rotate freely around the C1-C2 bond. (I wrote to you
> > about this too).
> > In short, NAMD can simulate butane just fine, but your assumption that you
> > can have a large enough rigid section (more than 3 atoms) is incorrect.
> > Please, do try with a molecule that includes a rigid group like a benzyl
> > ring. (See my previous email).
> > Thank you
> > Giacomo
> > On Sun, May 11, 2014 at 5:52 PM, nicolas martin <
> > nicolasmartin973_at_gmail.com> wrote:
> >> 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)
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