From: nicolas martin (nicolasmartin973_at_gmail.com)
Date: Thu May 22 2014 - 06:21:02 CDT
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
> 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,
>> 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.
>>> ----- 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
>>> > use spinangle covlar to compute a PMF along the rotation of the
>>> > 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
>>> > 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
>>> > PMF and the one obtained with a simple dihedral colvar (my reference)--089e0160b420e1a9a004f9fb4edc--
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