Re: AMBER: SHAKE Problem

From: David A. Case <>
Date: Wed, 6 Aug 2003 14:52:21 -0700

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:
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            |
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Received on Wed Aug 06 2003 - 22:53:00 PDT
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