From: Narasimhan LOGANATHAN (Narasimhan.Loganathan_at_etu.univ-provence.fr)
Date: Mon Mar 18 2013 - 13:37:45 CDT
Thanks for the reply. I would do the constraints according to your suggestions.
I will update on my progress.
> From: Jérôme Hénin <jerome.henin_at_ibpc.fr>
> Sent: Mon Mar 18 18:04:03 CET 2013
> To: Narasimhan LOGANATHAN <Narasimhan.Loganathan_at_etu.univ-provence.fr>
> Subject: Re: namd-l: distanceZ - harmonic restraints
> 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.
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