On Fri, Feb 01, 2013, Joe Passman wrote:
>
> If I make the box
> bigger (i.e. box length = 60 ang), the boxes of water look like they are
> stacking on top of each other.
Yes, there appears to be a bug in solvateBox if the buffer size gets really
big. Note that a command like "solvatebox l100 TIP3PBOX 60" gives a box size
of about 120 Ang (not 60), and close to 500,000 atoms, which is enormous by
Amber standards, and is probably why no one has seen this problem before.
I'd be surpised if a 20 Ang. buffer is too small. Note that if you just do
minimization, nothing will move very much: you would have to run (lots of) MD
to see a peptide have a major change in shape. You might also try solvateOct,
which gives a more spherical shape (and hence is more appropriate for most
structural changes. I don't know if solvateOct has the same limitations as
solvateBox.
We'll look in to what is going on with the solvateBox command. Thanks for the
report.
...regards...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jan 31 2013 - 19:00:02 PST
