From chemistry-request "-at-" ccl.net Wed Jan 7 08:24:29 2004 Received: from postbode01.zonnet.nl (postbode01.zonnet.nl [62.58.50.88]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i07DNvX9029991 for ; Wed, 7 Jan 2004 08:23:58 -0500 Received: (qmail 2860 invoked by uid 10); 7 Jan 2004 13:23:56 -0000 Received: (vexira-qq 02851-6F3EE432 invoked from network) 07 Jan 2004 14:23:55 +0100 Received: from unknown (HELO chem.vu.nl) ([62.59.65.24]) (envelope-sender ) by postbode01.zonnet.nl (qmail-ldap-1.03) with SMTP for < >; 7 Jan 2004 13:23:55 -0000 Message-ID: <3FFBE795.4050106.-at-.chem.vu.nl> Date: Wed, 07 Jan 2004 12:03:49 +0100 From: Anton Feenstra Reply-To: feenstra.-at-.chem.vu.nl User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.4.1) Gecko/20031008 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Rick Venable CC: Wei Shi , chemistry.-at-.ccl.net Subject: Re: CCL:CCL References: In-Reply-To: Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-AntiVirus: checked by Vexira MailArmor (version: 2.0.1.16; VAE: 6.23.0.2; VDF: 6.23.0.22; host: postbode01.zonnet.nl) X-Spam-Status: No, hits=-2.6 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Rick Venable wrote: > For a solvated protein simulation, I'd monitor the potential energy, the > radius of gyration, and the bacbone RMSD relative to the starting > structure. When all 3 of these become flat, one could argue that > the system is equilibrated; this could require 100s of picoseconds. Although indeed one can argue this, it is hard to tell what 'flat' means in a practical sense. For a seond-year lecture I give I have three slides each giving the rmsd of a protein w/r to the x-ray structure. All three of them level off to a nice plateau at the end, and appear to be genuinly equilibrated in the way you define that. But, the three plots are of the same simulation, the first of 0-100ps, the second of 0-1ns, and the last of 0-10ns! If you overlay them, they are almost the same, except for the scale of the axes! Those of you who'd like to see them, please ask me and I can send you the three jpg files (~50k each). While I don't regularly monitor r_gyr or e_pot, I don't know but suspect that they would show similar behaviour... (although they may equilibrate much faster than the rmsd). -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 | | | Feenstra.-at-.chem.vu.nl - www.chem.vu.nl/~feenstra/ | | | "If You See Me Getting High, Knock Me Down" | | | (Red Hot Chili Peppers) | |_____________|_______________________________________________________|