AMBER Archive (2003)

Subject: RE: AMBER: SHAKE Problem

From: Richard Smith (dicksmit_at_umich.edu)
Date: Thu Aug 07 2003 - 09:42:56 CDT


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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of David A. Case
Sent: Wednesday, August 06, 2003 5:52 PM
To: amber_at_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_at_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 ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu

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