PBC

From: Werner Crous (crous.werner_at_gmail.com)
Date: Wed Jun 01 2011 - 05:09:27 CDT

Dear NAMD-users

I have a problem with imaging in NAMD. I used a truncated octahedron within
the NVT ensemble. What happened was that after 12ns the protein only
partially moved out of the truncated octahedron, but my one substrate was
imaged right to the other side of the box. This then looks as if the
substrate moved out of the protein, but I assume it is just the imaging. The
susbstrate is imaged differently to the protein. As a CHARMM user, I know
that one can specify if you want the imaging to happen by segment or by
residue, but in NAMD I am not aware of such options. How does imaging work
in NAMD for a TOH and what is the cutoff for the minimum imaging convention?

Thank you in anticipation.

Best regards
Werner

-- 
Werner Crous
Scientific Computing Research Unit
University of Cape Town
Rondebosch 7701
South Africa
Phone: +27 21 650 2530 (O)
Fax: +27 21 686 4333
http://scru.uct.ac.za
http://scientificomputing.com

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