From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Oct 01 2015 - 07:11:45 CDT
Hi Nicolas,
> If I am right, the axis direction specified by the user is translated to
the center of mass of the selection on which the Spinangle is applied to
perform the rotation. Which then makes the the extracellular part rotate
around the predefined axis going through its center of mass.
The rotational coordinates in colvars are designed to separate out
rotational and translational degrees of freedom, that is, so that
rotational biases exert zero net force on the center of geometry
(essentially the same as the center of mass). The result might be a
rotation around the center of mass if the system is freely tumbling. But if
it is anchored to another object with a flexible link or a hinge, then
rotation around the hinge or around the center of the rotating group are
the same thing in terms of rotational degrees of freedom.
In principle you can apply a rotational bias, and let the translational
degrees of freedom relax, resulting in rotation around the hinge. The fact
that you are not seeing that could mean that the bias is applied too far
from equilibrium, so that translational degrees of freedom don't have time
to relax. For this kind of application you may be better off with something
like targeted MD. Or you could rephrase the problem in translational terms,
eg. distances between groups of atoms.
Jérôme
On 1 October 2015 at 12:13, Nicolas Martin <nicolasmartin973_at_gmail.com>
wrote:
> Dear Namd users,
>
> Here is what I wish to do: I have a protein composed of two domains, one
> trans-membrane and one extracellular, and 5 subunit arrange to form a pore
> in the middle. I would like to force my extra cellular domain to radially
> expend. In other words, I want the extracellular domain to bend in an
> outward position as a flower would do when it blooms. Final goal being to
> perform a PMF of that reaction coordinate.
>
> I was told by Jérôme Hénin, that cosine of the tilt angle is unsigned and
> thus one cannot use it for such application. And indeed I tried and it did
> not work, the rotation being inward. I tried to use Spinangle and found out
> it might not fully answer my question neither. If I am right, the axis
> direction specified by the user is translated to the center of mass of the
> selection on which the Spinangle is applied to perform the rotation. Which
> then makes the the extracellular part rotate around the predefined axis
> going through its center of mass. Which is not what I am aiming for.
>
> Is there any possibility/keyword to unset that auto translation to the CoM
> or even better to translate it to another point or COM of another selection
> ? Do you see any other colvar that I could use for doing such thing ?
>
> Thanks a lot for your help,
>
> Cheers,
>
> Nicolas Martin
>
>
>
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