Re: Zcoord-1atom for ABF

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Thu Nov 25 2010 - 02:42:47 CST

Hi Parisa,

> I am a little confused with the definition of "abf coordinate zCoord-1atom"
> in tutorial when using ABF.

Some of the information you are referring to is outdated. The current
tutorial is there:
http://www.ks.uiuc.edu/Training/Tutorials/#adbias

> I know that "zCoord-1atom" corresponds to the distance separating an atom
> and a group of atoms along the z-direction of Cartesian space. My system
> consists of an ion moving in a channel and I want it to move just along Z
> not x and y directions.

Then you need restraints in (x, y): for that, use a collective
variable of type distanceXY.

Cheers,
Jerome

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