Protein-ligand complex is coming out of the water box

From: Nancy Singh (
Date: Wed Jul 14 2021 - 06:16:58 CDT

I have done the protein-ligand simulations with namd for 10ns. But the
problem is after 5ns protein and ligand complex starts to move out of the
box. I have already put wrapALL, wrapNearest and wrapWater as ON but still
the complex is coming out of the box. Is there something wrong with
simulations or it is natural for protein to move from one periodic cell to
and How can I tackle this if I want to make th animation of my trajectory?

Thank You


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