how to keep the atom's trajectory within the box

王胜杰 theancientg... at
Fri Mar 18 16:41:40 UTC 2016

Dear all

When I was dealing with the trajectory of MD, I found the atoms always move 
beyond the boundary, making some atoms' coordinate larger than the box 
length,which reflect the true trajectories. 
But I don't want a true trajectory, I want a periodic boundary.When the 
atoms cross the boundary, the coordinate will minus the box length 
automatically, which each direction of  atoms' coordinate is less than the 
box length. By adding what command line can I fix that?

Thanks in advance.
Shengjie Wang 
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