Periodic boundary conditions

From: Gianluca Interlandi (
Date: Fri Nov 30 2007 - 19:20:07 CST

Dear community,

I have run a simulation with NAMD using 150 mM of NaCl. I used

wrapAll off
wrapWater on

I noticed that the ions move out of the the primary cell because they
don't get wrapped around. The simulation lasted 40 ns. Is this a problem?
I know that the ions are internally wrapped around, but does it work
correctly even if they fly far away from the primary cell? I also
restarted the simulation after every ns. Could this give a problem?

Thanks a lot,


Dr. Gianluca Interlandi
                    +1 (206) 685 4435
                    +1 (206) 714 4303

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.

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