Dmitry,
did you use iwrap=1 ?
this will image the waters back into the main box.
You can also use ptraj to postprocess the trajectory and
image the water. In any case the simulatino is fine, it is just
a question of viewing convenience vs. being able to calculate
diffusion with the real (non-imaged) coords.
Carlos
----- Original Message -----
From: <dkon_at_email.arizona.edu>
To: <amber_at_heimdal.compchem.ucsf.edu>
Sent: Wednesday, July 18, 2001 7:20 PM
Subject: AMBER box
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
Received on Thu Jul 19 2001 - 04:24:35 PDT
