From chemistry-request(+ at +)ccl.net Sat Jan  3 13:25:03 2004
Received: from glaurung.gpcc.itd.umich.edu (glaurung.gpcc.itd.umich.edu [141.211.2.181])
	by server.ccl.net (8.12.8/8.12.8) with ESMTP id i03IOVTC004703
	for <chemistry[at]ccl.net>; Sat, 3 Jan 2004 13:24:31 -0500
Received: from asteroids.gpcc.itd.umich.edu (asteroids.gpcc.itd.umich.edu [141.211.2.218])
        by glaurung.gpcc.itd.umich.edu (8.9.3p2/4.3-mailhub) with ESMTP id NAA07554
        for <chemistry[at]ccl.net>; Sat, 3 Jan 2004 13:24:27 -0500 (EST)
Received: from localhost (weishi-: at :-localhost)
	by asteroids.gpcc.itd.umich.edu (8.9.3p2/5.1-client) with ESMTP id NAA27230
	for <chemistry[at]ccl.net>; Sat, 3 Jan 2004 13:24:27 -0500 (EST)
Precedence: first-class
Date: Sat, 3 Jan 2004 13:24:27 -0500 (EST)
From: Wei Shi <weishi[at]umich.edu>
X-X-Sender: weishi[at]asteroids.gpcc.itd.umich.edu
To: chemistry[at]ccl.net
Subject: CCL
Message-ID: <Pine.SOL.4.58.0401031313590.26464[at]asteroids.gpcc.itd.umich.edu>
MIME-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII
X-Spam-Status: No, hits=0.0 required=7.0
	tests=USER_AGENT_PINE
	version=2.55
X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp)

Dear CCLers,

Happy new year!

I have one question for CHARMm about equilibration. Generally, the
calculation is started from the X ray structure, then heating,
equilibrating by velocity scale, and lastly production run without
velocity scale in the NVE MD simulation. However, I found that many of the
authors do not check the system to make sure it has been equilibrated
before they take the production run. Fro example, Some authors observe the
temperature  is increasing with the potential energy drifting down in the
production run. However, they still do the analysis. Is that a problem?

Thanks for all your help,

Wei Shi