From rochus@felix.anorg.chemie.tu-muenchen.de Thu Jun 8 11:03:08 1995 Received: from felix.anorg.chemie.tu-muenchen.de for rochus@felix.anorg.chemie.tu-muenchen.de by www.ccl.net (8.6.10/930601.1506) id KAA09907; Thu, 8 Jun 1995 10:49:16 -0400 Received: by felix.anorg.chemie.tu-muenchen.de (940816.SGI.8.6.9/930416.SGI) id QAA10767; Thu, 8 Jun 1995 16:47:52 +0200 From: "Rochus Schmid" Message-Id: <9506081647.ZM10765@felix> Date: Thu, 8 Jun 1995 16:47:51 -0600 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@ccl.net Subject: Molec. Mech. Program in C Cc: rochus@felix.anorg.chemie.tu-muenchen.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCL people, I recently posted the following question: > Does anyone of you know a (PD) Molecular Mechanics program written in C > with the source code freely available? It can be any simple diagonal > forcefield together with any optimizer. I just want to plug some extra > terms in and test them. I've got a large feedback of people who wanted to know my results. It seems, there is a need. Here is all I've got yet: (Thanks to Craig Burkhart, Andreas Windemuth, Konrad Hinsen and Carlos A. Del Carpio) 1.) PMD On May 22, 10:36am, Andreas Windemuth wrote: > Subject: Re: CCL:Molecular Mechanics program in C > > You could try the program PMD, a parallel molecular dynamics > program with the fast multipole algorithm. Look for it under the > URL "http://tincan.bioc.columbia.edu/pmd/". > > --- > Andreas Windemuth > > +-------------------------------------------------------------------- > |Columbia University, Department of Biochemistry and Biophysics > |630 West 168th St. BB-221 | tel: (212)-305-6884, fax: 6926, NeXTmail > |New York, NY 10032 | email: windemut@cumbnd.bioc.columbia.edu > +-------------------------------------------------------------------- >-- End of excerpt from Andreas Windemuth 2.) There is a Molec. Mechanics and Dynamics Program available (with sources) for academic users from CCP in Daresbury (UK): ftp.dl.ac.uk in /ccp5 http://www.dl.ac.uk/CCP/CCP5/main.html But it is in FORTRAN !!!!!! (But they claim to have a well structured code) 3.) In Journal of Computational Chemistry 1993, Vol. 14, 455-470 Robert K.Z. Tan and Stephen C. Harvey describe their Molecular Mechanics Program called Yammp, which is in C and developed by a modular programming method. Thus it seems to be perfectly suited for adding own potential functions. Unfortunately I don't know if the code is available and I don't know their E-mail adress. If someone knows their E-mail, please tell me! (By the way: it would really be helpfull, if JCC would include it in the authors adress). 4.) Carlos A. Del Carpio is on the way to translate MM2 to C. He allowed me to put that in this summary. For details please contact him. carlos@translell.tutkie.tut.ac.jp Thanks again to all, who replied on my question. Greetings from Munich to all out there. Rochus Schmid -- ******************************************************************************** Rochus Schmid Technische Universitaet Muenchen Tel. ++49 89 3209 3140 Anorganisch Chemisches Institut 1 Fax. ++49 89 3209 3473 Prof. W. A. Herrmann E-mail: Lichtenbergstrasse 4 rochus@felix.anorg.chemie.tu-muenchen.de 85747 Garching ******************************************************************************** From YU@msvax.mssm.edu Thu Jun 8 13:48:19 1995 Received: from msvax for YU@msvax.mssm.edu by www.ccl.net (8.6.10/930601.1506) id NAA13976; Thu, 8 Jun 1995 13:39:41 -0400 From: Received: from msvax.mssm.edu by msvax.mssm.edu (PMDF V4.3-7 #2473) id <01HRGRG6H0XC00374X@msvax.mssm.edu>; Thu, 8 Jun 1995 13:40:26 EST Date: Thu, 08 Jun 1995 13:40:26 -0500 (EST) Subject: Graphics Software for Zincblende Materials To: chemistry@ccl.net Message-id: <01HRGRG6HC8200374X@msvax.mssm.edu> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Netter: Our group are doing some MD simulations of zincblende-structured semiconductors, such as GaAs, Ge and Si. We are interested in getting or buying some visualization software packages on SGI for displaying the geometry structure of such materials. Could someone point out to me what there are and where I can get? I will summarize to the net. Thanks in advance. Wenbin Yu From swm@osiris.rti.org Thu Jun 8 14:48:11 1995 Received: from rccw21.rti.org for swm@osiris.rti.org by www.ccl.net (8.6.10/930601.1506) id OAA15591; Thu, 8 Jun 1995 14:43:20 -0400 Received: from osiris.rti.org by RCCW21.RTI.ORG (PMDF V4.3-13 #8058) id <01HRGTMTR180005RER@RCCW21.RTI.ORG>; Thu, 08 Jun 1995 14:43:04 -0400 (EDT) Received: from thoth.rti.org by osiris.rti.org via SMTP (931110.SGI/930416.SGI.AUTO) for @rccw21.rti.org:chemistry@ccl.net id AA01138; Thu, 8 Jun 95 14:38:05 -0400 Date: Thu, 08 Jun 1995 14:42:53 -0400 From: Wayne Mascarella Subject: mol2pov To: CCL Message-id: X-Mailer: VersaTerm Link v1.1.4 Content-transfer-encoding: 7BIT Has anyone been able to compile Andreas Dominik's mol2pov utility on an SGI system under IRIX 5.x? Wayne Mascarella swm@osiris.rti.org (919) 541-8810 MCB 279 Chemistry & Life Sciences / Organic & Medicinal Chemistry Research Triangle Institute, North Carolina 27709 USA From PUDZIANOWSKI@bms.com Thu Jun 8 17:03:13 1995 Received: from cliff.bms.com for PUDZIANOWSKI@bms.com by www.ccl.net (8.6.10/930601.1506) id RAA18063; Thu, 8 Jun 1995 17:02:52 -0400 From: Received: from conan.bms.com by cliff.bms.com (PMDF V4.3-10 #9246) id <01HRGYI2RXNK005ZPG@cliff.bms.com>; Thu, 08 Jun 1995 17:02:01 -0500 (EST) Received: from bms.com by bms.com (PMDF V4.3-7 #5676) id <01HRGYHT4G0G8YADL2@bms.com>; Thu, 8 Jun 1995 17:01:48 EST Date: Thu, 08 Jun 1995 17:01:48 -0500 (EST) Subject: AIM graphics software? To: chemistry@ccl.net Message-id: <01HRGYHT5ILE8YADL2@bms.com> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Friends and fellow scholars, Does anyone know of a program or programs that will permit quantities associated with the atoms-in-molecules theory, e.g., zero-flux atomic boundary surfaces and so on, to be displayed graphically? Such software might be compatible with PROAIMS, or the new AIM properties modules in Gaussian 94. Barring that, could someone feed me some hints as to how to get started in trying to write my own program? I'm not thinking about anything fancy: just getting an output file that could be contoured would be wonderful. If someone points me in the right direction in the PROAIMS code, which I have, maybe I can come up with something workable. If anyone gets the urge to respond, please do so directly to me and I'll summarize if there's enough interest. Best wishes, Andy Pudzianowski *********************************************************************** Andrew T. Pudzianowski,Ph.D. Bristol-Myers Squibb PRI Box 4000 * "There are two ways to do things. Princeton NJ 08543-4000 * There's the scientific way, and (609) 252-4248 * there's the disgusting way." (609) 252-5747: fax * pudzianowski@bms.com * "Beakman's World", 1994 ***********************************************************************