Re: distanceZ - harmonic restraints

From: Jérôme Hénin (
Date: Mon Mar 18 2013 - 12:04:03 CDT

Hi Naresh,

> 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.


This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:23:03 CST