AMBER Archive (2002)

Subject: Re: Density during equilibration (sander)

From: David A. Case (case_at_scripps.edu)
Date: Tue Sep 17 2002 - 14:21:49 CDT

On Tue, Sep 17, 2002, Pratul Agarwal wrote:
>
> I can try it, I was avoiding longer NPT simulations because the goal in
> the longer run is to study protein dynamics. In a previous post you had
> mentioned that temperature baths and pressure pistons distort the
> system and thats why I was avoiding longer NPT simulations.

You should make a distinction between equilibration and production runs. You
need enough NPT equilibration to get a good density and temperature, but you
don't analyze results from that. After getting the right density, you can
switch to NVE for the production part, which is where you look at dynamics.

..hope this helps...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
==================================================================