Re: Unsure about current setting of Periodic Boundary Conditions

From: Diego Alejandro Vargas (vardiego9_at_gmail.com)
Date: Tue Dec 23 2008 - 18:58:03 CST

Peter,
Thank you for your reply. I am unsure as to whether I do not want periodic
boundary conditions. As I wrote, when I look at the dcd file for the
periodic boundary conditions simulation once part of the protein exits the
water box, this part appears on the opposite side. Would this not make it
interact with the protein on an adjacent cell and affect the behavior of the
pulling?

Also, the slowing down: The simulation with periodic boundary conditions is
completed in ~18h and seems to take place at a steady pace. The non-periodic
one I am still running, has been running for 2d in which it first stated it
would take 17h and currently says it has 134h left (and increasing).

Diego

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