From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Mar 18 2013 - 12:04:03 CDT
> However, during the course of the simulation, the vector moves along
> the XY plane at the centered Z-position.
> I understand that only the Z component is constrained and not XY.
> My doubts are
> 1) why the vector is moving along the XY plane when the axis keyword
> for x and y are set to be 0.0
It's exactly as you said, the restraints only apply along z, so motion along x and y is free.
> 2) Since, there is a constant movement along the XY plane, does it
> still hold the atom identities for distance measurements.
I think the answer is yes, although I am not perfectly sure that I understand your question.
> 3) I think that this motion has a strong influence on sampling the
> regions specific to the defined sites.
> 4) how to avoid this and to keep the XY motions to minimum and to
> have calculate the PMF for the specified sites on the substrate.
You could apply a restraint on a distanceXY coordinate. That is a natural complement to distanceZ, when one thinks of a problem in cylindrical coordinates. The restraint could be a harmonic potential centered on zero, or it could be an upper limit set by the upperWall keyword.
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