From chemistry-request@server.ccl.net Thu Dec 26 19:51:52 2002 Received: from pacific-carrier-annex.mit.edu ([18.7.21.83]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBR0pqh09972 for ; Thu, 26 Dec 2002 19:51:52 -0500 Received: from grand-central-station.mit.edu (GRAND-CENTRAL-STATION.MIT.EDU [18.7.21.82]) by pacific-carrier-annex.mit.edu (8.9.2/8.9.2) with ESMTP id TAA10430 for ; Thu, 26 Dec 2002 19:51:51 -0500 (EST) Received: from manawatu-mail-centre.mit.edu (MANAWATU-MAIL-CENTRE.MIT.EDU [18.7.7.71]) by grand-central-station.mit.edu (8.9.2/8.9.2) with ESMTP id TAA00982 for ; Thu, 26 Dec 2002 19:49:43 -0500 (EST) Received: from buzzword-bingo.mit.edu (BUZZWORD-BINGO.MIT.EDU [18.7.16.73]) by manawatu-mail-centre.mit.edu (8.9.2/8.9.2) with ESMTP id TAA17405 for ; Thu, 26 Dec 2002 19:49:43 -0500 (EST) Received: from localhost (damians@localhost) by buzzword-bingo.mit.edu (8.9.3) with ESMTP id TAA12491; Thu, 26 Dec 2002 19:49:42 -0500 (EST) Date: Thu, 26 Dec 2002 19:49:42 -0500 (EST) From: Damian A Scherlis Perel To: Subject: code to solve Poisson-Boltzmann Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I am interested in a subroutine or package to solve numerically in a grid elliptic partial differential equations (in particular the Poisson-Boltzmann equation). I have been trying with the multigrid code of Michael Holst released in 1995, but it shows serious inaccuracies in R3 for the kind of trial potentials I used to test it. Is anyone aware of some other code suitable for this? Many thanks, and happy holidays, ------------------------ Damian Scherlis Department of Materials Science & Engineering Massachusetts Institute of Technology damians@mit.edu 617 253 6026 From chemistry-request@server.ccl.net Thu Dec 26 15:52:01 2002 Received: from billthecat.sdsc.edu ([132.249.20.60]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBQKq0h07688 for ; Thu, 26 Dec 2002 15:52:01 -0500 Received: from sudholt2k (sudholt-2k.sdsc.edu [132.249.98.80]) by billthecat.sdsc.edu (8.11.6/8.11.6/mx/34) with ESMTP id gBQKpuC18579; Thu, 26 Dec 2002 12:51:57 -0800 (PST) From: "Wibke Sudholt" To: "Lommerse, J.P.M. \(Jos\)" Cc: Subject: RE: Constrained geometry optimisation with GAUSSIAN98 Date: Thu, 26 Dec 2002 12:51:52 -0800 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) In-Reply-To: <639D20177889D41198A600508BAD3CA1039AD2DD@capella3.oss.akzonobel.nl> X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Importance: Normal Hello, you will not be able to find a true energy minimum (with no imaginary frequencies) as long as you constrain any intramolecular geometric parameter in your molecule to a value different from the equilibrium one. This is due to the fact that the vibrational analysis is usually done on all (internal or cartesian) coordinates together, which are transformed into normal coordinates (employing a multidimensional harmonic/parabola picture of the energy minimum). When one or more coordinates are far from their optimum values in the final structure (which will probably be the case when you constrain them), imaginary frequencies are the result. Thus you may either live with that, perform a full geometry optimization without constraints, or include a description of the environment that deforms your molecule into the desired conformation. I hope this helps, Wibke Sudholt University of California, San Diego wibke@sdsc.edu -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On Behalf Of Lommerse, J.P.M. (Jos) Sent: Friday, December 20, 2002 1:37 AM To: 'chemistry@ccl.net' Cc: Vuuren, M. van (Marlous) Subject: CCL:Constrained geometry optimisation with GAUSSIAN98 Hello, I am trying to optimize the geometry of small organic molecules while keeping fixed all dihedral angles at certain values around rotatable bonds. Whatever optimization procedure (Berny, Steep, etc.) I apply, or start conformation I choose, the optimization fails to arrive at a true local minimum, viz. the resulting geometry always contains one or more imaginary frequencies. Does anybody know how to get to a true local minimum while applying these dihedral angle constraints? Here's an simple problem molecule example com-file for GAUSSIAN98 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ %chk=pdb35.chk # rhf/PM3 Molecule pdb35 (1isi_NCA_1) 0 1 N 6.3300 42.5360 90.0450 C 5.1180 41.9260 90.5820 C 3.9970 42.7130 90.9900 C 4.1850 44.1520 90.8210 C 5.3590 44.7550 90.2990 C 6.4330 43.9350 89.9100 C 2.6760 42.1220 91.5670 O 1.7720 42.8950 91.8870 N 2.5360 40.8370 91.7060 H 5.0663 40.8412 90.6744 H 3.3664 44.8083 91.1165 H 5.4271 45.8385 90.2010 H 7.3421 44.3799 89.5054 H 3.3010 40.2032 91.4339 H 1.6602 40.4528 92.0883 --Link1-- %chk=pdb35.chk #T rhf/PM3 geom=(checkpoint,modify) opt=modredundant * * A * * * A * * * * A * 3 7 * F ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Thanks a lot, Jos Lommerse jos.lommerse@organon.com Dr Ir Jos Lommerse, Research Scientist Molecular Design & Informatics, N.V. 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If you receive this message in error or if it is intended for someone else please notify the sender by returning this e-mail immediately and delete the message. -------------------------------------------------------------------- -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Thu Dec 26 20:39:43 2002 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBR1dhh10272 for ; Thu, 26 Dec 2002 20:39:43 -0500 Received: from arlen.ccl.net (arlen.ccl.net [192.148.249.10]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id gBR1dfj05940 for ; Thu, 26 Dec 2002 20:39:41 -0500 (EST) Date: Thu, 26 Dec 2002 20:39:40 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net Subject: 2003.05.18 Intelligent Processing & Manufact of Materials Message-ID: MIME-Version: 1.0 Content-ID: ---------- Forwarded message ---------- Date: Fri, 27 Dec 2002 00:01:03 +0900 From: Hiroshi Mizuseki Reply-To: ipmm@imr.edu To: ipmm@imr.edu Subject: IPMM'03 --> Dear all, The IPMM'03 conference (The 4th International Conference on Intelligent Processing and Manufacturing of Materials) will be held in Sendai, Japan, May 18-23, 2003. To know more about IPMM'03, please visit the website http://www-lab.imr.tohoku.ac.jp/~ipmm/ where you will find useful information. *** IMPORTANT *** Extension of Abstract Submission Deadline: December, 31st. Please be informed that the deadline for abstract submission has been extended to 31 December 2002. --- Planned Sessions I. Focus Sessions: Nanotechnology Molecular Electronics - molecular wires, switches, and circuits - simulation Carbon-based New Materials - Fullerenes, Carbon Nanotubes, and other structures - Applications Clusters (other than carbon) - silicon, metal, and other clusters - applications Advanced Silicon Technology - Si/SiO2 interface - surface chemistry Atomic-level Measurement and Manipulation - STM, AFM, and X-Rays Micro-Electronic Machines Nano-Sensors and Instruments Biomaterials - Protein Engineering - DNA as an Element of Molecular Engineering - Mechanisms Next-Generation Computing Systems - Quantum and DNA Computing II. Standard Sessions: Intelligent Processing and Manufacturing Simulation Modeling - new materials and property prediction - materials processing and product manufacturing - supervisory and process control Agent-based Modeling - holonic systems and intelligent manufacturing - Swarm Intelligence and Artificial Life - optimization versus incremental improvements - local vs. global decision-making Software and "Soft" wear - Fuzzy Logic, Neural Networks, Evolutionary Programming, and Chaos Theory - Intelligent User Interfaces Robotics and Machines - mini- and micro-machines - telerobotic applications - remote communication systems (outer space and underground applications) Processes for the 21st Century - raw materials production systems (mining and processing) - metals production and forming - finishing and final-shape processes The Philosophy of Intelligence in New Materials and Processes - Nature of intelligence - Transhumanism and the Machine Age --- If you have any question regarding the IPMM'03 conference, please feel free to contact me. We much look forward to hearing from you soon. Best Regards, Hiroshi Mizuseki (ipmm@imr.edu) (on behalf of the local organizing committee) http://www.kawazoe.imr.edu/ http://www-lab.imr.edu/~mizuseki/ PS. If you have already submitted an abstract please disregard this message From chemistry-request@server.ccl.net Thu Dec 26 20:58:49 2002 Received: from billthecat.sdsc.edu ([132.249.20.60]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBR1wmh10484 for ; Thu, 26 Dec 2002 20:58:49 -0500 Received: from sudholt2k (sudholt-2k.sdsc.edu [132.249.98.80]) by billthecat.sdsc.edu (8.11.6/8.11.6/mx/34) with ESMTP id gBR1wkC23816; Thu, 26 Dec 2002 17:58:47 -0800 (PST) From: "Wibke Sudholt" To: "Damian A Scherlis Perel" Cc: Subject: RE: code to solve Poisson-Boltzmann Date: Thu, 26 Dec 2002 17:58:44 -0800 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) In-Reply-To: X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Importance: Normal Hello, perhaps you may take a look at APBS: http://agave.wustl.edu/apbs/ I hope this helps, Wibke Sudholt University of California, San Diego wibke@sdsc.edu -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On Behalf Of Damian A Scherlis Perel Sent: Thursday, December 26, 2002 4:50 PM To: chemistry@ccl.net Subject: CCL:code to solve Poisson-Boltzmann Dear all, I am interested in a subroutine or package to solve numerically in a grid elliptic partial differential equations (in particular the Poisson-Boltzmann equation). I have been trying with the multigrid code of Michael Holst released in 1995, but it shows serious inaccuracies in R3 for the kind of trial potentials I used to test it. Is anyone aware of some other code suitable for this? Many thanks, and happy holidays, ------------------------ Damian Scherlis Department of Materials Science & Engineering Massachusetts Institute of Technology damians@mit.edu 617 253 6026 -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net