about interaction between protein and its image in namd simulation

From: Liqun Zhang (lxz79_at_case.edu)
Date: Tue Jul 09 2013 - 12:16:37 CDT

Dear namd users:

I set up a rectangular box to solvate a protein complex (dimer) using water
molecules. The size of the box is like following: 90 A, 80 A, and 70 A. The
cutoff is around 12 A. Since the complex can do random global movements
inside the box, can the rectangular box cause any extra interaction between
the protein and its image once the longest axis of the complex aligned to
the shorted side? Thank you very much.

Best regards,


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