AMBER: solvatebox vs solvateoct

From: Francesco Pietra <>
Date: Sun, 25 Nov 2007 10:27:06 -0800 (PST)

It is known (David Cerutti 31Aug97) that with systems largely non-cubic,
solvatebox places fewer solvent molecules than solvateoct.

This is my case with a protein complex in a lipidic membrane. With a 12.0A
buffer (too much? see below) solvatebox added 21808 TIP3 WAT (density 0.793),
while solvateoct added 29815 (density 0.867).

Is it obvious that solvatebox is the choice here to carry out MD? I wonder
about the initial densities.

Being at such a system for the first time, I have no idea how much it will
shrink during equilibration, i.e. if the protein-complex will emerge too much
from the membrane. Usually, as far as I can remember, the choice of the buffer
(see 12.0A above) should be judged from the longest atom to atom distance, i.e.
the solvation box should be larger that such a distance increased of the
cutoff.In this case it is not obvious to determine such atom-to-atom distance,

francesco pietra

Get easy, one-click access to your favorites.
Make Yahoo! your homepage.
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Nov 28 2007 - 06:07:06 PST
Custom Search