Colvars periodic boundary treatment question

From: Kasra Fattah (
Date: Sat Nov 30 2013 - 13:12:42 CST

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?


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