Periodic Box Size vs. Water Box Size

From: Seth Lilavivat (
Date: Thu Feb 28 2008 - 10:33:04 CST

Dear NAMD users,

I have a fairly basic question as a new NAMD user. Should your perodic box
size be as close as possible to the size of your water box? If you are
wrapping waters, does it not make sense then to have a periodic box size
that is slightly smaller than your water box to ensure there is no vacuum in
between water and periodic boundary?


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