From: JC Gumbart (
Date: Wed Feb 16 2011 - 07:49:41 CST

A cheap hack - you could manually shift the coordinates of those protein
atoms outside the box by one cell length and then find the overlapping
waters. Or you could run solvate on this new (but otherwise useless) PDB
and use psfgen to delete the protein segment and then readd the original,
non-shifted protein.

I must concur though that it would need to be a very strange (and large)
system for this to be worth doing...

-----Original Message-----
From: [] On Behalf Of
Sharlene Denos
Sent: Wednesday, February 16, 2011 12:04 AM
Subject: vmd-l: PBC & Solvate Tool in VMD


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!