about long namd trajectory and pbc effect

From: Liqun Zhang (lxz79_at_case.edu)
Date: Sun Dec 02 2012 - 14:53:24 CST

Dear namd users:

I have run a very long namd simulation for a protein complex (2 proteins
binded) in a water box to observe the protein complex separation process.
Because of the pbc effect, I unwrapped the simulation trajectory. So I no
longer see one protein jumped at the edge of the box frequently. But the
unwrapped trajectory showed part of the protein outside of the water box.
Now I like to calculate the interaction between protein and the surrounding
water. Since one protein is partially outside of the box, I can not select
water around it. Then what I should do with that? Do I have to readjust the
simulation trajectory? If yes, how to show waters around the protein
outside of the box using pbc command in vmd? Any suggestion is welcomed.
Thanks a lot.

Best regards,


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