From chemistry-request@ccl.net Sun Jan 4 01:21:13 2004 Received: from gothmog.gpcc.itd.umich.edu (gothmog.gpcc.itd.umich.edu [141.211.2.180]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i046KgX9015189 for ; Sun, 4 Jan 2004 01:20:42 -0500 Received: from asteroids.gpcc.itd.umich.edu (asteroids.gpcc.itd.umich.edu [141.211.2.218]) by gothmog.gpcc.itd.umich.edu (8.9.3p2/4.3-mailhub) with ESMTP id BAA29640; Sun, 4 Jan 2004 01:20:41 -0500 (EST) Received: from localhost (weishi@localhost) by asteroids.gpcc.itd.umich.edu (8.9.3p2/5.1-client) with ESMTP id BAA12856; Sun, 4 Jan 2004 01:20:41 -0500 (EST) Precedence: first-class Date: Sun, 4 Jan 2004 01:20:41 -0500 (EST) From: Wei Shi X-X-Sender: weishi:at:asteroids.gpcc.itd.umich.edu To: Rick Venable cc: chemistry:at:ccl.net Subject: Re: CCL:CCL In-Reply-To: Message-ID: References: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-2.5 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi, Rick, Thanks for your help. Actually, my simulation is started from the PDB, which includes crystalized water, ion, protein, and ADP. I add missing residuals, and hydogen atoms. I assign potential type and partial charge for one of the residuals which does not exist in the rtf file in the CHARMm. Then, I do some steps of minization. In my system, I have not added solvent water and not applied the PBC. The total number of atoms is around 7000. I heat my system in 5 ps from 240 K to 300 K, then perform equilibration for 5 ps. After that, I perform 150 ps of NVE MD simulation production run. The time step is 0.001 ps. The potential energy is still drifting down in the production run. For example, I calculate the average potential in a time slot of 30 ps and the average is -17506 kcal/mol, the value for the next 30 ps is -17527 kcal/mol. This energy drift, I suppose, is not significant. The average difference is 0.1% in 30 ps. By the way, I have tried NVT MD simulation. The potential energy is still drifting down even after 700 ps. Generally, how long does it take to get equilibration from your experience if you start the simulation from the X ray structure? I have read many papers to hope to see the potential energy versus time without sucess. Can you give me some reference papers? Thanks very much for your help, Wei Shi On Sat, 3 Jan 2004, Rick Venable wrote: > 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 > =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= > From chemistry-request@ccl.net Sun Jan 4 16:19:58 2004 Received: from web20904.mail.yahoo.com (web20904.mail.yahoo.com [216.136.226.226]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i04LJRX9007616 for ; Sun, 4 Jan 2004 16:19:27 -0500 Message-ID: <20040104211924.29350.qmail_at_web20904.mail.yahoo.com> Received: from [68.155.80.163] by web20904.mail.yahoo.com via HTTP; Sun, 04 Jan 2004 13:19:24 PST Date: Sun, 4 Jan 2004 13:19:24 -0800 (PST) From: Anatoli Korkin Subject: classical MM/MD and tight binding studies of SiOx systems, 0