Questions on periodic boundary condition

From: LEWYN LI (
Date: Thu Sep 02 2004 - 00:38:24 CDT

         I just have two questions that I hope someone could help me with:

1. I am pulling a protein in SMD, and I see that some of the sidechains are
moving out of the water box during the simulation movie. Since I was using
periodic boundary condition, I am confused if these sidechains are truly out of
the box, or are the sidechains still solvated by (invisible) image water

2. Our protein is pretty big, and there are only 1 - 2 water layers above and
below the protein after equilibration. With periodic boundary condition, I
understand that this would mean there will be only 2 - 4 water layers between
the protein and its image in another cell. Is my understanding correct? And
what kind of artifacts may this introduce into the simulation?

         Thank you very much for your help!

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