Outward tilting which colvar to use

From: Nicolas Martin (nicolasmartin973_at_gmail.com)
Date: Thu Oct 01 2015 - 05:13:01 CDT

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,


Nicolas Martin

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