How to solve the out of cell box for long time in Periodic Boundary Conditions?

From: Aurum Bai (
Date: Wed May 19 2010 - 21:06:38 CDT

Hello, everyone.
I use namd to simulate the protein and ligand for long time. Then I found the ligand vanish at the boundary of cell box, while appear another boundary, but the protein not. The problem is normal, because I use the "Periodic Boundary Conditions".
But It brings some problem to calculate the rmsd and  binding energy and so on, because the coordnates of ligand had been changed.
How do I deal with this problem, and calculate the rmsd correctly?

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