From chemistry-request@server.ccl.net Tue Mar 5 04:49:40 2002 Received: from relay-4v.club-internet.fr ([194.158.96.115]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g259nd529195 for ; Tue, 5 Mar 2002 04:49:39 -0500 Received: from sungam (vlp8a-12.n.club-internet.fr [212.195.14.12]) by relay-4v.club-internet.fr (Postfix) with SMTP id 1191D16CF for ; Tue, 5 Mar 2002 10:49:04 +0100 (CET) Message-ID: <008d01c1c42c$16033a80$0c0ec3d4@sungam> From: "Julien MICHEL" To: Subject: Linear scaling QM calculations -summary- Date: Tue, 5 Mar 2002 10:56:52 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2919.6600 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 If someone is interested by this, here is a compilation of the links/references i received on the subject of Linear scaling algorithms for QM calculations. > From Andrew Horsfield : A good overview of the theory can be found in the review article Stefan Goedecker, Reviews of Modern Physics 71, 1085 (1999) For data on performance for quantum chemistry applications, the papers of Gustavo Scuseria are useful. For example: J. M. Millam and G. E. Scuseria, Journal of Chemical Physics 106, 5569 (1997) A. Daniels and G. Scuseria, Journal of Chemical Physics 110, 1321 (1999) K. Nemeth and G. Scuseria, Journal of Chemical Physics 113, 6035 (2000) > From Ed Brothers : Our lab has developed linear sclaing Semiempirical code for modeling sizable protiens and slovated systems at the (admittedly low) QM level. The relevent refrerences are: J Chem Phys, 1996, 104, 6643-9. J Chem Phys, 1997, 107, 879-93 > From Cherif F. Matta Matta, C.F. (2001) "Theoretical reconstruction of the electron density of large molecules from fragments determined as proper open quantum systems: The properties of morphine, the oripavine PEO, and enkephanlins". J. Phys. Chem. A, 105, 11088-11101. > From Sam Abrash This is state of the art work, and is still under development. Several labs in the world are working on this development. One of the best is the Berkeley group of Professor Head-Gordon. I believe that they have linear scaling working for Hartree-Fock, and are trying to extend it to correlated methods. Best regards, Sam Abrash > From Dr Martin Schuetz For coupled cluster methods with linear scaling check references on my web site http://www.theochem.uni-stuttgart.de/~schuetz/ > From David Gallagher One recent publication suggests that the frontier orbitals on the hydrated enzyme (calculated by MOPAC 2000) correlate to the active sites. See: Effects of Hydration on the Electronic Structure of an Enzyme: Implication for Catalytic Function, Kazuki Ohno et al, J. Am. Chem. Soc. 2001, 123, 8161-8162 A MOPAC 2002 SCF on Crambin (641 atom protein) takes less than 3 minutes on a 1,000 MHz Windows PC and uses only 60 MB of memory. MOPAC 2002 with the MOZYME linear scaling algorithm handles up to 20,000 atoms, for full geometry optimizations and reaction coordinates, and includes the COSMO solvent field. The algorithm also scales approximately linearly in memory usage. MOPAC 2002 is available stand-alone or as part of CAChe software suite. As the method is fairly new, there are not many publications on it's application to proteins around just yet. However, there is more information at www.cachesoftware.com > From Kris Van Alsenoy You may want to look at the following paper : Ab-initio geometry detreminations of proteins : 1. Crambin J. Phys. Chem. A, vol. 102, p2246-2251 (1998) > From Matt Challacombe Hi Julien, You can have a look at our web site (www.t12.lanl.gov/~mchalla), which is woefully out of date (will bring it to the present soon). It does however have some background papers that you may find relevant. We have a fully O(N) code that is getting close to beta quality, which does the following in TRUE O(N) for 3-D insulating systems: Orthogonalization, solution of SCF equations, exact exchange, exchange-correlation and Coulomb sums. It does geometry optimization and PBCs for pure DFT. -Matt > From Huud Van Dam Yes, linear scaling is possible at least for methods and in the limit of infinitely large molecules. There is still a lot of work being done in this field as the size of molecule at which linear scaling is "achieved" influences the total cost of the calculation (the sooner you reach linear scaling the cheaper the method, unless the prefactors differ dramatically of course). Places to start: - The group of Prof. Martin Head-Gordon: http://www.cchem.berkeley.edu/~mhggrp/ - The group of Prof Peter Gill: http://maclaurin.chem.nott.ac.uk/ Although their webpages aren't very clear about it they have done work on so called "attenuated Coulomb operators" but I am not sure what the current concensus on that approach is. - Then there is the Siesta program http://www.uam.es/departamentos/ciencias/fismateriac/siesta/ And there is a lot of material science stuff (you could do a search at www.google.com on "order-N"). I hope these pointers are something of a start. Best wishes, From chemistry-request@server.ccl.net Tue Mar 5 11:06:22 2002 Received: from vytautas.vdu.lt (mail@[193.219.38.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g25G6L503265 for ; Tue, 5 Mar 2002 11:06:21 -0500 Received: from vaidila.vdu.lt ([193.219.38.52] ident=root) by vytautas.vdu.lt with esmtp for chemistry@ccl.net id 16iHRh-0004SQ-00; Tue, 05 Mar 2002 18:05:45 +0200 Received: from TYREX (vejas.vdu.lt [193.219.38.82]) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id SAA03355 for ; Tue, 5 Mar 2002 18:05:36 +0200 (GMT) Date: Tue, 5 Mar 2002 18:05:51 +0200 From: a3arzi X-Mailer: The Bat! (v1.44) UNREG / CD5BF9353B3B7091 Reply-To: "Art'" X-Priority: 3 (Normal) Message-ID: <10512514184.20020305180551@vaidila.vdu.lt> To: chemistry@ccl.net Subject: CCL: DOCK -- about receptor Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello CCL'ers, Do we need include in structure all hydrogens preparing macro molecule - receptor - for DOCK ? -- Best regards, Arturas Z. mailto:a3arzi@vaidila.vdu.lt http://biologija.vdu.lt/person/ziemar/index.html From chemistry-request@server.ccl.net Tue Mar 5 12:29:32 2002 Received: from soul.helsinki.fi ([128.214.3.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g25HTV504900 for ; Tue, 5 Mar 2002 12:29:31 -0500 Received: from localhost (mpjohans@localhost) by soul.helsinki.fi (8.9.3/8.9.3) with ESMTP id TAA26053; Tue, 5 Mar 2002 19:28:54 +0200 (EET) X-Authentication-Warning: soul.helsinki.fi: mpjohans owned process doing -bs Date: Tue, 5 Mar 2002 19:28:54 +0200 (EET) From: Mikael Johansson X-Sender: To: Phil Hultin cc: Computational Chemistry List Subject: Re: CCL:Gaussian, Electron Density and AIM In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello Phil and All! On Mon, 4 Mar 2002, Phil Hultin wrote: > Dave Shobe wrote: > > >Come to think of it, I vaguely remember some kind of function, related to > >AIM analysis (atoms-in-molecues, based on the eletcron density > distribution) > >that had a maximum in lone pair regions of a molecule. > > Dave is referring to the Laplacian of the electron density, which can be > interpreted in terms of electron pair densities. The short introduction to > AIM by Paul Popelier (a paperback book, roughly 150 pages as I recall) > discusses this idea in some detail. Popelier has some information on his web page too: http://www.ch.umist.ac.uk/popelier.htm There is also a good AIM-introduction by Bader on the net: http://www.chemistry.mcmaster.ca/aim/ > I am not a disciple or anything, but if one is trying to dissect the charge > distribution in a molecule, it appears to me that AIM is probably the best > way to do it. At least, it has the virtue of being based on mathematically > rigorous analysis of the calculated or observed electron density. It does > not impose any pre-conceptions on how charge is assigned to atoms. Well, there is of course the postulate that specific gradient trajectories define the interatomic surfaces. It seems, to me at least, a very fair and plausible assumption, but an assumption nevertheless. Some problems with AIM are also discussed in the very good "Introduction to Computational Chemistry" by Jensen. Have a nice day, Mikael Johansson University of Helsinki Department of Chemistry mikael.johansson@helsinki.fi http://www.helsinki.fi/~mpjohans Phone: +358-9-191 50185 FAX : +358-9-191 50169 From chemistry-request@server.ccl.net Tue Mar 5 13:49:03 2002 Received: from server.nybc.org ([209.10.103.101]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g25Imw506003 for ; Tue, 5 Mar 2002 13:49:03 -0500 Received: from asim-lap.nybc.org ([172.16.1.226]) by server.nybc.org (Sun Internet Mail Server sims.4.0.2000.10.12.16.25.p8) with ESMTPA id <0GSI00B1NK1MR2@server.nybc.org> for chemistry@ccl.net; Tue, 5 Mar 2002 13:44:26 -0500 (EST) Date: Tue, 05 Mar 2002 13:41:30 -0500 From: "Dr. Asim K. Debnath" Subject: Re: CCL:DOCK -- about receptor In-reply-to: <10512514184.20020305180551@vaidila.vdu.lt> X-Sender: asim_debnath@server.nybc.org To: a3arzi@vaidila.vdu.lt Cc: chemistry@ccl.net Message-id: <5.1.0.14.0.20020305133653.00a6fec0@server.nybc.org> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Version 5.1 Content-type: text/plain; format=flowed; charset=us-ascii Content-transfer-encoding: 7BIT Hi Arturas: If you are using Dock4.0, you need to add hydrogen to ALL ATOMS since "grid needs them to identify VDW atom types". Please see the manual under "Preparing the Receptor File". Hope this helps. Good luck! Asim Debnath At 06:05 PM 3/5/02 +0200, a3arzi wrote: >Hello CCL'ers, > >Do we need include in structure all hydrogens preparing macro molecule >- receptor - for DOCK ? > > >-- >Best regards, >Arturas Z. > >mailto:a3arzi@vaidila.vdu.lt >http://biologija.vdu.lt/person/ziemar/index.html > > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net Asim K. Debnath, Ph.D. Associate Member New York Blood Center 310 E 67th Street New York, NY 100021 Tel. (212) 570-3373 E-mail: asim_debnath@nybc.org