From: Sharlene Denos (
Date: Wed Feb 16 2011 - 00:03:36 CST


I am trying to run a NAMD simulation using periodic boundary conditions (PBC). My initial configuration includes a water box that is slightly smaller than the total span of the proteins solvated. This should not be a problem for the simulation due to the use of PBC except that the water box does not have room for the proteins to wrap around on the other side. I created my water box using the Solvate plugin in VMD and I did not see an option for PBC. Does this exist? If not, what's the easiest way to figure out which waters need to be deleted from my system in order to make room for the protein to be wrapped around?

Thank you!