Re: Colvars periodic boundary treatment question

From: Kasra Fattah (
Date: Sat Nov 30 2013 - 22:25:46 CST

Thanks for your response Jerome.
I also tried using "period" and "wrapAround" options with "period 50" and
"wrapAround 0.0" (basically the default value of wrapAround) in distanceZ
and I used the unwrapped coordinates for the walls positions, i.e.
"lowerWall 20" and "upperWall 30". It seems that it's working too, is that
a legit treatment of the problem or not? (btw, I'm using a dummy atom as a
reference group at position (0.0, 0.0, 0.0) )

One more question:
I'm actually doing a 1D ABF calculation and my reaction coordinate is Z
direction of the cartesian system. But in order to limit the simulation in
x and y directions I'm defining two other reaction coordinates, x and y.
The sole application of these two reaction coordinates are for using their
"lowerWall" and "upperWall" options to enforce the molecule remains in the
desired window in x and y directions but I'm not using them in free energy
calculation part of abf, i.e. just using "colvars z" in the abf part of the
config file. I was wondering if this is a right way of confining the
molecule in the directions that I'm not doing free energy calculations?


On Sat, Nov 30, 2013 at 7:04 PM, Jrme Hnin <> wrote:

> Hi Kasra,
> The best way for this is to use distanceZ with a reference group close to
> the region of interest (if you want an absolute position along the axis, it
> would be a dummy atom group, and you can choose its position arbitrarily)--001a11c3c7dc107c6604ec7175d0--

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