Re: Colvars periodic boundary treatment question

From: Jérôme Hénin (
Date: Sat Nov 30 2013 - 19:04:48 CST

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).
In the case you describe in your message, you could define a distanceZ component with the reference group as a dummy atom at (0, 25, 0), in which case the lowerWall would be -5 and upperWall would be 5. You don't need to worry about PBC, as they will be enforced automatically, because the distance between your molecule and the dummy atom will be computed following the minimum image convention.

That's why the distanceZ coordinate is not explicitly treated as periodic by default: the minimum image convention for distances usually does the job well.


----- Original Message -----

> Hi All,
> I've got a question regarding the treatment of a reaction coordinate that
> crosses a periodic boundary.
> If I want to confine the center of mass of a molecule between two points
> along, let's say, y axis which crosses the periodic boundary in that
> direction how should I define lowerWall and upperWall? for example if the
> box size in y direction is from -25 to 25 and initially the com of the
> molecule is located at y=25 but I want it to be confined in y-direction +/-
> 5 from its initial position. Based on unwraped values it should be between
> 20 and 30, i.e. "lowerWall 20" and "upperWall 30" but I'm not sure if I have
> to use unwrapped coordinates or wrapped ones?!

> I Would appreciate it if you could help me to know how I should set these
> values...There are also two options in the manual "period" and "wrapAround"
> should I also set them (i.e. "period 10" and "wrapAround 25")? or they are
> not related to what I need?

> Cheers,
> Kasra.

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:57 CST