From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Mon Feb 14 2011 - 16:04:27 CST
Dear Jérôme and Giacomo,
if points A and B of the dihedral angle are the are the positions of two
atoms and points C and D two dummy atoms, then the orientation of the plane
normal BC will oscillate with the thermal movement of B.
But I would much prefer to have the plane normal fixed. I could try setting
the BC distance to a very large value (then the movement of B will not
change the orientation of BC that much), but I don't know if it is possible
to set a dummy atom outside of the periodic cell boundary.
Otherwise I would kindly ask for a colvar component in which the two axes
can be fixed in space (with axis and planeAxis).
Thank you & best regards,
2011/2/14 Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>
> Thank you both!
> This is a great idea and I think I should be able to get the desired
> result, since I'm "cheating" a bit and restraining the rotation of the
> protein so that I can use fixed reference axes :)
> So now I only have to derive the jacobian for the angle colvar and I'm on
> my way.
> Best regards,
> 2011/2/14 Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>
> Hi Ajasja,
>> The coordinate you describe seems closely related to a torsional angle
>> ("dihedral"). The torsional angle defined by points A-B-C-D is the
>> angle between vectors BA and CD, projected onto a plane whose normal
>> is BC. So it is likely that the existing "dihedral" component could be
>> easily adapted to do what you need. Another consequence is that the
>> Jacobian contribution is zero.
>> The more annoying part seems to be the logic, since there are many
>> ways the axes can be defined. I don't have specific usage cases in
>> mind, so it's hard to narrow things down.
>> 2011/2/14 Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>:
>> > Dear NAMD developers,
>> > After a lot of thought I have come to the conclusion that I would really
>> > need to sample my system along a colvar similar to the phi component of
>> > polar coordinates.
>> > The colvar would measure the angle between the projections of a vector
>> > a reference vector on a plane.
>> > A suitable name for the colvar component would be either angleProjection
>> > angleXY.
>> > It could except the following parameters:
>> > main and ref to define the main (measured) vector.
>> > ref2 or axis to define the reference vector
>> > ref3 and ref4 or planeAxis to define the normal vector of the plane.
>> > most probably ref3 and ref would be the same for most cases... Also
>> > more discriptive names then ref1, ref2 etc could be used? Perhaps ref1
>> > ref2 for the refrence vector and planeRef1 and planeRef2 for the plane
>> > normal?
>> > The main and the reference vectors are projected to the plane and the
>> > between them is returned as the value of the colvar. The angle would be
>> > the range of [0°,360°) or (-180°, +180°] measured in the positive
>> > orientation from the reference to the main vector.
>> > Would somebody be willing to help me implement this in NAMD?
>> > I volunteer to derive the Jacobian in analytical form (needed for ABF),
>> > I woudl be really glad if somebody could write the C part.
>> > Thank you for your help & best regards,
>> > Ajasja Ljubetič,
>> > Young reasercher,
>> > Laboratory of biophysics,
>> > Institute Jožef Štefan,
>> > Ljubljana, Slovenia
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