hole on the surface of the waterbox

From: Mert Gür (gurmert_at_gmail.com)
Date: Fri Aug 28 2009 - 05:08:09 CDT

Dear all,
I am performing MD simulation of crambin in a large waterbox (20 A cushion)
with periodic boundary conditions. I don't use any rigid bonds.

When I load my dcd file it seems that there is a hole on the surface where
there are no watermolecules. But I came to this conclusion simply looking at
the video. The protein stays in the middle of the waterbox during the

Does that mean there is anything wrong with my simulation? Can this kinda
behaviour happen for the water solvent? Is there a fast way to check if
there really is a hole without looking at the video file (Maybe the video
is just misleading me; there is no hole)?
I attached my conf file in case you want to check it.


This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:13 CST