My protein went out of the water box in SMD. Would it have a bad effect on the result?

From: wayj86 wayj86 (
Date: Fri Jun 26 2009 - 03:02:46 CDT

Dear all,

I found it is difficult to make sure the protein keep in the water box
during the whole SMD process unless with a very big box. Now my protein went
out of the box with more than 10 residues and 14 angstrom off the water
boundary in the -Z direction. The distance between the "went-out" part and
the protein in the next cell was 13 angstrom. I have red the NAMD tutorial
but still want to ask you some questions:

(1) Althought the protein should be merged in the water box when imposing
periodic boundary conditions, was the "went_out" phenomenon completely

(2) In my situation, would it have a bad effect on my result? Do I have to
redo the SMD again?

(3) Is there any literature about this phenomenon which explain it in

Thank you in advance.

The future is now!

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