AMBER Archive (2001)

Subject: AMBER box

From: dkon_at_email.arizona.edu
Date: Wed Jul 18 2001 - 18:20:00 CDT

Hello,

I couldn't find the answer to this on the list archive, although I believe
this has been raised before: why does it look like waters escape from
the box during a constant-pressure simulation? Comparing the starting
and ending coordinates in MolView (after 1ns), it looks like most waters

are no longer solvating the protein, but instead are in outer space.
However, I used a box with periodic boundaries, and the overall density
remained constant (1.1 g/cm^3) So what is the problem? Thank you very
much in advance,
Dmitry