Thank you very much Mr. Case and Mr. Periole,
Equilibration to the final temperature with constant volume was
successful.
Richard Smith
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
Of David A. Case
Sent: Wednesday, August 06, 2003 5:52 PM
To: amber.scripps.edu
Subject: Re: AMBER: SHAKE Problem
On Wed, Aug 06, 2003, Richard Smith wrote:
>
> I am using sander_classic of AMBER6 to equilibrate a protein in an
> octahedral box of TIP3P water. I am using periodic boundary
conditions
> with constant pressure to increase the temperature from 50 - 310K in
50
> K increments at 10 ps each with a 0.002 ps time step
You can't do this. You need to equilibrate a constant volume to the
desired
temperature, and *then* turn on constant pressure to get the density
adjusted.
It's not clear that this is causing your problem, but it is certainly
worth
a try.
....good luck....dac
--
==================================================================
David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
==================================================================
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Received on Thu Aug 07 2003 - 15:53:01 PDT
