From chemistry-request@www.ccl.net Tue Apr 13 07:36:05 1999 Received: from ct2.mpibpc.gwdg.de (ct2.mpibpc.gwdg.de [134.76.213.214]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA21746 Tue, 13 Apr 1999 07:35:44 -0400 (EDT) Received: (from gkaeb@localhost) by ct2.mpibpc.gwdg.de (AIX4.2/UCB 8.7/8.7) id NAA13060; Tue, 13 Apr 1999 13:34:45 +0200 (MESZ) Date: Tue, 13 Apr 1999 13:34:45 +0200 (MESZ) From: Guenter Kaeb Message-Id: <199904131134.NAA13060@ct2.mpibpc.gwdg.de> To: chemistry@www.ccl.net Subject: Flexible MD code wanted Cc: gkaeb@gwdg.de Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-MD5: 0h+sHa0FZGV2kBA4Fupl1w== Dear CCLers, I would be very glad if somebody could point me to freely available MD code (Fortran 90 or C) which is flexible enough to treat general interaction potentials between molecular degrees of freedom. General properties should in principle comprise the following features: Our specific aim is to simulate by molecular dynamics (completely classical in the initial stage) the vibrational cooling process of a small linear triatomic in an atomic (rare gas) solvent. The complete nuclear potential energy surface for the triatomic (CO2) known from high-resolution vibrational spectroscopy is of high accuracy involving polynomial expansion terms up to the sixth order and should ideally be fully included. Of special importance are the off-diagonal terms in the Hamiltonian which lead to energy exchange between vibrational modes. Such coupling terms are, however, rarely included in general purpose MD programs suited to treat large (bio-)molecules and complex solvents for which detailed information on molecular interaction terms going beyond harmonic or Morse potentials is seldom available or not needed to describe structures and processes of interest. What we are looking for is MD code, which is suited to address smaller molecules in simpler solvents, but with higher accuracy. As stated above, intramolecular potentials should go beyond non-interacting localized bonding terms. Also, van der Waals pairwise interaction potentials for solvent sites should be able to involve more parameters than e.g. the well-known Lennard-Jones potential. In the most general case, the forces may be derived numerically from the potentials specified as input. It would be nice, however, to evaluate forces analytically were possible, which is quite easy for polynomial expansions mentioned above, and more accurate of course. Knowing that the complete list of properties is probably not realized by any existing AND freely available MD package without the need for additional programming and modification for our own purposes, I would be glad to receive information on any modularly designed package or bunch of routines which would allow for more or less "straightforward" adaptation without having to program from scratch basic standard MD ingredients such as periodic boundaries (cubic will be sufficient) or ensemble realizations (NVE, NpT, ...) etc. Finally, I am looking forward to hearing from you! Kind regards, Guenter Kaeb ============================================================================== = = = Dr. Guenter Kaeb = = Max-Planck-Institute of Biophysical Chemistry = = (Department 010: Spectroscopy and photochemical kinetics) = = Am Fassberg 11 = = D-37077 Goettingen = = = = Tel.: +49-551/201-1344 = = Fax: +49-551/201-1006 = = = = e-mail: gkaeb@gwdg.de = = = ============================================================================== From chemistry-request@www.ccl.net Tue Apr 13 09:23:03 1999 Received: from chm-pluto.ulaval.ca (chm-pluto.ulaval.ca [132.203.2.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id JAA23049 Tue, 13 Apr 1999 09:23:03 -0400 (EDT) Received: from OXYGENE (unverified [132.203.70.8]) by serveur_chimie.chm.ulaval.ca (EMWAC SMTPRS 0.83) with SMTP id ; Tue, 13 Apr 1999 09:22:55 -0400 Date: Tue, 13 Apr 1999 09:22:55 -0400 Message-Id: <3.0.16.19990413092255.0ef7589a@serveur_chimie.chm.ulaval.ca> X-Sender: mroberge@serveur_chimie.chm.ulaval.ca X-Mailer: Windows Eudora Pro Version 3.0 (16) To: chemistry@www.ccl.net From: Mathieu Roberge Subject: Biosym Command Language (for macros in InsightII) Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id JAA23050 Hi there ! I am looking for documentation about the BCL (Biosym Command Language) used in InsightII for the programming of macros. The manual from MSI do contain something, but the ones I got are quite old (v4.0.0.). I'm interested in anything that might be of use (command list, examples, etc.). Mathieu Roberge ---------------------------------------------------------------------------- -------------------------- Dept. Chimie, Université Laval 2450 Place Prével, #2 Cite universitaire, Ste-Foy Ste-Foy, Québec Quebec, Canada, G1K 7P4 G1V 2X3 (418) 656-2131 poste 4210 (418) 650-7199 ---------------------------------------------------------------------------- -------------------------- Mathieu.Roberge@chm.ulaval.ca From chemistry-request@www.ccl.net Tue Apr 13 10:39:36 1999 Received: from mail.candseek.com (mail.candseek.com [209.146.77.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA23932 Tue, 13 Apr 1999 10:39:36 -0400 (EDT) Date: Tue, 13 Apr 1999 10:39:36 -0400 (EDT) From: 915613@candseek.com Message-Id: <199904131439.KAA23932@www.ccl.net> Received: from candseek.com ([209.146.77.254]) by mail.candseek.com (Post.Office MTA v3.5.1 release 219 ID# 0-55033U100L2S100V35) with SMTP id com for ; Tue, 13 Apr 1999 10:30:45 -0400 To: chemistry@www.ccl.net Subject: JOBOP Molecular Biology Scientist Since your email address was listed on a related web site page or database, I thought you might help. 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Your email address will be permanently filtered from ALL future job opportunity notifications sent via the Candidate Seeker system. To temporarily filter employment opportunity notices sent via the Candidate Seeker system, type the acronym "JOBOP" into your subject filter. All employment opportunity notices sent via the Candidate Seeker system contain the acronym "JOBOP" in the subject so they may be easily filtered or blocked if so desired. Other email addresses may be permanently deleted from future contact by emailing a single blank message from the desired address to nomail@candseek.com. Enter additional addresses into the body of the message and they will also be added to the "nomail" list Please feel free to contact the candidateseeker.com feedback line at 609-584-5499. Do not use this number for job related questions. All job related questions should be directed to the employer by replying to contact addresses or phone numbers indicated at the end of the job description message. From chemistry-request@www.ccl.net Tue Apr 13 10:39:43 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA23939 Tue, 13 Apr 1999 10:39:42 -0400 (EDT) Received: from mail.candseek.com (mail.candseek.com [209.146.77.10]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id KAA18002 for ; Tue, 13 Apr 1999 10:39:36 -0400 (EDT) Date: Tue, 13 Apr 1999 10:39:36 -0400 (EDT) From: 915613@candseek.com Message-Id: <199904131439.KAA18002@ccl.net> Received: from candseek.com ([209.146.77.254]) by mail.candseek.com (Post.Office MTA v3.5.1 release 219 ID# 0-55033U100L2S100V35) with SMTP id com for ; Tue, 13 Apr 1999 10:30:46 -0400 To: chemistry@ccl.net Subject: JOBOP Molecular Biology Scientist Since your email address was listed on a related web site page or database, I thought you might help. I am seeking an individual within the following conditions: A scientist to work in a lab that is working with technology development systems that deal with gene regulation in viruses. The candidate should have a very strong background in Molecular Biology focusing on mechanisms of eukaryotic transcription regulation and experience with high level expression of recombinant proteins in mammalian cells. This position will focus on all aspects of mammalian expression. We would like to explore and develop new expression vectors for transient and stable expression, new selection and amplification methods, and evaluate/develop new expression systems. Much of this work currently involves evaluation of expression by FACS. The ideal candidate will also develop systems that facilitate the study of structure/function relationships in ligand-receptor models. The candidate should possess a PhD degree in the Biological Sciences, 3 years postdoctoral experience and between 2 and 5 years industrial experience. Our client is a leading bio-tech company with research facilities in Westchester County, New York and can provide excellent benefits (health insurance, dental, and vision plan, paid vacation and more). A high impact, high profile position with excellent opportunity for advancement. Geographic Location of Position: US-NY If you know anyone that might be interested, please forward this to them or contact: Barry Gilfillan Diedre Moire Corporation Voice: 609-584-8733 Ext. 235 Fax: 609-584-9575 Email: 915613@candseek.com To permanently discontinue receiving employment opportunity notices from any and all help wanted advertisers using the Candidate Seeker system, click your "Reply" button and type the word "re- move" without spaces between the letters into the SUBJECT field then click the "Send" button. Your email address will be permanently filtered from ALL future job opportunity notifications sent via the Candidate Seeker system. To temporarily filter employment opportunity notices sent via the Candidate Seeker system, type the acronym "JOBOP" into your subject filter. All employment opportunity notices sent via the Candidate Seeker system contain the acronym "JOBOP" in the subject so they may be easily filtered or blocked if so desired. Other email addresses may be permanently deleted from future contact by emailing a single blank message from the desired address to nomail@candseek.com. Enter additional addresses into the body of the message and they will also be added to the "nomail" list Please feel free to contact the candidateseeker.com feedback line at 609-584-5499. Do not use this number for job related questions. All job related questions should be directed to the employer by replying to contact addresses or phone numbers indicated at the end of the job description message.