From: Sharlene Denos (
Date: Wed Feb 16 2011 - 08:37:30 CST

Thanks JC & Ajasja. That will work perfectly.

And yes, my system is strange. It reflects my experimental conditions in which the protein concentration is close to the saturation point!

Thanks again for the advice!


On Feb 16, 2011, at 7:49 AM, JC Gumbart wrote:

> 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
> To:
> Subject: vmd-l: PBC & Solvate Tool in VMD
> Hello,
> 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!
> Sharlene

Sharlene Denos, PhD
K-12 Outreach Coordinator
Center for The Physics of Living Cells
University of Illinois at Urbana-Champaign
1110 West Green Street, MC-704
Urbana, IL 61801 USA
(217) 244-0672