From chemistry-request[ AT ]ccl.net Sat Jan 3 19:29:02 2004 Received: from kafka.net.nih.gov (kafka.net.nih.gov [165.112.130.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i040SUTC009846 for ; Sat, 3 Jan 2004 19:28:30 -0500 Received: from pollux.cber.nih.gov (pollux.cber.nih.gov [128.231.52.5]) by kafka.net.nih.gov (8.12.10/8.12.9) with ESMTP id i040SRcD020740; Sat, 3 Jan 2004 19:28:27 -0500 (EST) Date: Sat, 3 Jan 2004 19:17:50 -0500 From: Rick Venable To: Wei Shi cc: chemistry^at^ccl.net Subject: Re: CCL:CCL In-Reply-To: Message-ID: References: ReplyTo: Rick_Venable^at^nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-1.1 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT, RCVD_IN_NJABL,REFERENCES,REPLY_WITH_QUOTES,USER_AGENT_PINE, X_NJABL_OPEN_PROXY version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Certainly, a system with increasing T and decreasing potential energy is not at equilibrium, but obviously still relaxing. Depending on the magnitude of the drift and the analysis, the results may be misleading. Some additional notes about CHARMM usage-- NPT ensemble may be better, at least for equilibration after heating; a symmetric lattice such as cubic, truncated octahedron, or rhombic dodecahedron is usually appropriate for a solvated protein. I've observed quicker equilibration with velocity assignment (as opposed to velocity scaling). I guess it depends on your projects-- most of my CHARMM simulations start with coordinates from an extensive model building procedure On Sat, 3 Jan 2004, Wei Shi wrote: > 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? =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable^at^nih.gov ALT email: rvenable^at^speakeasy.org ------------------------------------- "Don't blame me, I voted for Kang." Homer =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=