From chemistry-request@ccl.net Thu Jul 9 01:29:31 1992 Date: Wed, 8 Jul 92 23:19:11 EDT From: Dongchul Lim Subject: Scientific computing To: chemistry@ccl.net (Computational Chemistry) Status: R Discussion on scientific computing is (was?) going on in sci.physics news group. Subject is "Scientific Computing" and it had ~40 replies. They look like fortran vs c++ (or other objected-oriented high-level languages) war, but some articles may be interesting to programmers in chemistry field. -dcl From chemistry-request@ccl.net Thu Jul 9 06:50:58 1992 Date: Thu, 9 Jul 92 09:25:02 BST From: Mark Forster To: CHEMISTRY Status: R Subject: AMBER Dear Comp. Chemists. When an AMBER MD run is performed using periodic boundary conditions at constant volume (NTB=1) the system pressure will vary from step to step. How can the pressure variations be found from the MD run? The sander.out file gives the energy breakdown thus: NSTEP = 300 TIME(PS) = 0.300 TEMP(K) = 272.56 PRESS = 0.00 Etot = -4347.9814 EKtot = 1381.1565 EPtot = -5729.1382 BOND = 1024.1494 ANGLE = 41.6554 DIHED = 17.5418 1-4 NB = 11.9262 1-4 EEL = 251.5237 NONBOND = 1154.6329 NBEEL = -8230.5684 EHBOND = 0.0000 CONSTRAINT = 0.0000 but there seems to be no easy way to get P fluctuations out. We typically have used a system in contact with a heat bath i.e. not classical dynamics where the sum of PE+KE is a constant. Any and all help gratefully received. Mark.Forster forster@comp.nibsc.ac.uk ps. sending message to CHEMISTRY%ccl.net@uk.ac.nsfnet-relay From chemistry-request@ccl.net Thu Jul 9 09:09:26 1992 Date: Thu, 9 Jul 92 11:47:40 BST From: Mark Forster To: CHEMISTRY Status: R Meeting announcement Molecular Graphics Society Autumn meeting. On the subject of 'Entropy and Solvation'. Brasenose College, University of Oxford, Oxford, UK. September 17th and 18th 1992. The Molecular Graphics Society will be holding an Autumn meeting on the topic of entropy and solvation effects in molecular modelling and computational chemistry. The meeting will be held in the pleasant surroundings of Brasenose College Oxford, with lectures taking place in the physical chemistry laboratory. The invited speakers and their presentations will include: Bill Jorgensen (Yale University), Molecular recognition in organic and biomolecular systems. Barry Honig, (Columbia University), Electrostatic and hydrophobic contributions to solvation free energies: application to binding and macromolecular stability. Anders Wallqvist (University of Lund), Hydrophobic aggregation in aqueous systems, Mike Frisch (Lorentzian Inc), Incorporation of solvent effects into electronic structure calculations. James Caldwell (University of California, San Francisco), Non additive effects on the structure and energetics of water, methanol and N-methylacetamide. The full meeting program will be sent out in a second mailing. Call for papers. Researchers who wish to present an oral contribution of approximately 30-40 minutes, or to exhibit a poster, are asked to submit a brief abstract of 300 words by fax, electronic or postal mail for consideration by co-organisers before July 24th. Notification of acceptance will be sent out by July 30th. Mark Forster, Howard Broughton, NIBSC, Merck Sharp Dohme, Blanche Lane, South Mimms, Terlings Park, Harlow, Herts. EN6 3QG. Essex CM20 2QR. tel (0707) 55753 (0279) 440500 fax (0707) 46730 (0279) 440390 e-mail: forster@uk.ac.nibsc.comp hbro@merck.com Communications with the organisers that are likely to be received in the first 3 weeks of August should be sent to Howard Broughton. Meeting fees / Application form. The meeting registration fee will be 70 pounds ($130 US) and accomodation in the college will be a further 70 pounds ($130 US). Cheques should be made payable to the 'Molecular Graphics Society' and drawn in pounds sterling or US dollars only. The accomodation fee includes a single room in Brasenose College on the nights of Wednesday 16th and thursday 17th, all meals on Thursday as well as breakfast and lunch on Friday. A limited number of college rooms with private bathrooms can be made available at an extra charge. A limited number of student bursaries will be available please contact one of the co-organisers before July 24th. Those wishing to register before the full meeting program is available please tick the option boxes below, detach and return the completed form. -------------------------------------------------------------------- Molecular Graphics Society Autumn meeting: I enclose the registration fee of 70.00 pounds / $130 US [ ] I enclose the accomodation fee of 70.00 pounds / $130 US [ ] Please send me a map/directions to Brasenose College, I enclose a stamped self addressed envelope. [ ] Specify any special requirements (diet etc). From chemistry-request@ccl.net Thu Jul 9 09:52:35 1992 Date: Thu, 9 Jul 92 14:16:21 WETDST From: dov@menora.weizmann.ac.IL (Dov Grobgeld) Subject: Looking for a 'PlotAtoms' program for RS/6000 To: chemistry@ccl.net (Computational Chemistry List) Status: R We are going to have an 'Open House' here in the chemistry department in November, and I would like to show some classical chemical dynamics simulation on our RS/6000 work station. I have a program called PlotAtoms which came with the Science Workbench suite of public domain programs from the Cornell university. It shows a movie of the motion of spheres. It receives as input a file (or standard input) of coordinates and color of all the atoms to plot. Each movie frame is separated by a new line. Unfortunately the frames are shown very 'jerky' on our RS/6000. I believe that if there was a similar program using the GL library the result would be much smoother. Is there any such program available for the RS/6000? Any GL program example source which shows how I can draw disks or spheres would also be very much appreciated. -- ___ ___ / o \ o \ Dov Grobgeld ( o o ) o | The Weizmann Institute of Science, Israel \ o /o o / Department of Chemical Physics | | | | "Where the tree of wisdom carries oranges" _| |_ _| |_ From flicker%rna.engin.umich.edu@srvr2.engin.umich.edu Thu Jul 9 12:54:50 1992 Date: Thu, 9 Jul 92 12:54:23 -0400 From: Scott Gregory Flicker To: chemistry@ccl.net, jkl@ccl.net Subject: Re: Forcefields archives idea Status: R I think the idea of having an online data bank of parameter would be very useful. IMHO, all that would be necessary would be a detailed description of each parameter set along with methods of usage, I don't think this would have to be more than say 5 pages of text. Along with this description would be the actual parameter set. I don't think the methods used to derive the parameter need given, and only references to the literature be listed. I think it would also be useful if working summaries/recipes for various common algorithms be available at the same site. If this basic set were done first than and the actual parameter sets could use this as a reference to shorten the detailed descriptions. Scott From chemistry-request@ccl.net Thu Jul 9 13:13:56 1992 Date: Thu, 9 Jul 92 08:40:52 -0500 From: molsol@wucmd.wustl.EDU (Molecular Solutions) Subject: Yellow Pages To: chemistry@ccl.net Status: R ***************************** FINAL NOTICE *********************************** This message was sent during the time the bulletin board was down. We have collected a lengthy list of entries for The Computational Chemistry Yellow Pages. However, we want to be sure our coverage is as complete as possible. Please send us notice of any software or services of interest to the community. Since our printing deadline is rapidly approaching, please respond as quickly as possible. The objective of this listing is to provide a general resource for groups starting to explore molecular modeling/computational chemistry as well as those who have been in the field for years. There is no charge for inclusion in the listing. You are free to describe your program/service (in 2 paragraphs if possible). Please provide contact information, pricing (optional), hardware supported, ... Thanks to all that have responded to date. Merry Ambos/Allen Richon/Bruce Gelin From chemistry-request@ccl.net Thu Jul 9 13:58:30 1992 Date: Thu, 9 Jul 92 08:42:03 -0500 From: molsol@wucmd.wustl.EDU (Molecular Solutions) To: chemistry@ccl.net Status: R Does anyone have an address/phone number for Angelo Vedani? Thanks Allen Richon From chemistry-request@ccl.net Thu Jul 9 15:44:15 1992 Date: 1-JUL-1992 09:16:32.01 From: WSONNEN@EAGLE.WESLEYAN.EDU Subject: CHARMm DNA cutoffs To: chemistry@ccl.net Status: R Dear Netters, I am interested in gathering information about DNA simulations using the CHARMm force field. In particular, i would like to know what cutoff algorithms (switching vs shifting), cutoff distances (including hydrogen bonding), etc were used. I would like to know this information for both vacuum and solvated (especially solvated!) simulations. I already know what is in the literature, so i don't need anything already published. What i would like is some feedback on results, by CHARMm users, on DNA (or relevant systems) that have not been published. I am working with CHARMm 21.3. I would prefer information on this force field, as the force fields in previous CHARMm versions are different. I have done some simulations on vacuum and solvated DNA with both the switching and shifting algorithms. I don't have the time or resources to do an extensive analysis on the cuttoff distances for switching vs. shifting algorithm. Along these lines, i must emphasize that i am interested in solvated simulations! Any input on your part would be greatly appreciated. This information is for my own purposes---helping me decide on what parameters to use in a DNA simulation. If there is enough input and enough interest, i will summarize the results on the net. Sincere thanks, Wayne Sonnen wsonnen@eagle.wesleyan.edu From chemistry-request@ccl.net Thu Jul 9 16:02:55 1992 Date: Thu, 9 Jul 92 08:53:56 CDT From: combariz@rouge.phys.lsu.EDU (Jaime Combariza) Subject: CRAY YMP EL To: CHEMISTRY@ccl.net, combariz@rouge.phys.lsu.EDU Status: R Hi. Has anybody had any experience running programs on the CRAY Y-MP EL using from 1-4 cpu's? In particular, we would like to know the performance of codes such as Gaussian 90 (or 92), GAMESS, and any type of Monte Carlo and/or Molecular Dynamics programs. Your information will be greatly appreciated Jaime E. Combariza combariz@bijou.chem.lsu.edu From chemistry-request@ccl.net Thu Jul 9 16:56:45 1992 Date: Thu, 09 Jul 92 16:00:31 CET From: "Dr. Piotr Paneth" Subject: AMPAC/MOPAC on Magnum To: CCList Status: R Dear Netters, does anyone have any experience with running Mopac or Ampac on MIPS ARCSystem Magnum R4000 (or R3000)? I'd appreciate any comments on performance and portability of these codes to the above platform. Thanks in advance, Piotr From chemistry-request@ccl.net Thu Jul 9 18:01:04 1992 Date: Thu, 9 Jul 1992 11:32 EST From: J_WILSON@CC.BRYNMAWR.EDU Subject: Molecular Dynamics To: chemistry@ccl.net Status: R Some in our group are beginning molecular dynamics studies on small organic compounds in solution. By small I mean less than about 60 heavy atoms. There is much in the literature on protein and other large biomolecular simulations, but we have come across very little so far dealing with smaller ring systems. Can some of you point us in the right direction with references, hints, etc. concerning any calculations done exploring dynamical behavior of compounds of this type in any solvent? It would be most appreciated. Please respond directly to me and I will summarize if needed. thanks in advance, J. Bundens Bryn Mawr College troi@galileo.brynmawr.edu From chemistry-request@ccl.net Thu Jul 9 18:46:41 1992 Date: Thu, 9 Jul 92 11:45:07 -0400 From: friedman@tammy.harvard.EDU (Dawn Friedman) Subject: gaussian wavefunctions To: chemistry@ccl.net Status: R I'm a bit mystified by the output of the STABLE keyword in Gaussian 90. Has anyone used this keyword to test the stability of their HF (especially UHF) wavefunctions? Once you've determined that your wavefunction _is_ unstable with respect to one or more factors, and used the stable=opt option to get a better wavefunction, what do you do next? For example, if the unstable wavefunction was the result of an geometry optimization, is it possible to get a better geometry from the better wavefunction in some way? What do you do with the better wavefunction other than admire it? And what do the various forms of instability "mean" in physical terms, if anything? Thanks, Dawn (friedman@tammy.harvard.edu) p.s. to jkl: thanks for letting us know. It's always unpleasant to be the bearer of evil tidings, or even moderately annoying tidings... From chemistry-request@ccl.net Thu Jul 9 19:21:17 1992 Date: Thu, 9 JUL 92 09:22:48 From: br1@inel.GOV Subject: position wanted To: chemistry@ccl.net Status: R Dear Friends: I am looking for a career position related to any one of the areas described below. Alternatively, I would gratefully accept a post doctoral position that would end in the fall of 1993. Currently, I am an AWU postdoctoral fellow, stationed at the Idaho National Engineering Laboratory. My contributions to the Laboratory have been divided between advances in theoretical chemistry and applications to important problems in materials science. In the year and a half I have been here I have enjoyed using techniques in electronic structure theory to study the phenomena of intercation, surface ionization, chemisorption, and thin-film polymer processing. Prior to coming here I completed my Ph. D. thesis under the advise of Dr. Lawrence Lohr at the University of Michigan. My time there was divided between; 1) research for my dissertation (oxides of nitrogen, phosphorus, and carbon; mostly NO3), 2) method and fortran code development for a group of space physicists who are interested in the concentration of selected excited state species of oxygen and nitrogen in the F-region of Earth's atmosphere, and 3) teaching a number of different courses, including one summer of lecturing at the University of Michigan in Flint. I must say that I have truly enjoyed all of these roles, but now I feel it is time for me to focus my career onto any one of these areas, or onto a related area of specialization. Below you will find a brief synapses of my vita. If you are interested in more detail on any of these topics, please call or write and I will get this information to you as soon as I can. Lest it be overlooked let me also point out that I have 15 years of experience in jobs not related to science, and a year and half experience working in a synthetic-organic lab for college credit. Randall C. Boehm born: 10/19/63 phone: (208) 526-8730 (work) 8-5 MDT (208) 529-9042 (home) any time e-mail: BR1@INEL.GOV addr: Theory Project, Chemical Sciences Idaho National Engineering Laboratory EG&G of Idaho, Inc. P. O. Box 1625 Idaho Falls, ID 83415-2208 ----Education---- B.S. University of Wisconsin at Madison (1985) M.S. University of Michigan at Ann Arbor (1988) Ph.D. University of Michigan at Ann Arbor (1991) ----Research History---- Undergraduate: synthetic-organic (1984-1985) Drs. Howard Zimmerman and Frank Oaks Graduate: theoretical (1986-1991) Dr. Lawrence Lohr Supporting: programer (1989) Drs. Vince Abreu and Ed Hume Postdoctoral: theoretical (1991-1992) Dr. Ajit Banerjee ----Teaching History---- UM-Ann Arbor: General Chemistry (one term) M. Halada and E. Westrum Organic Chemistry Lab (two terms) P. Smith Thermodynamics (three terms) J. Gland and R. Kopelman Quantum Mechanics (six terms) T.Dunn, S.Blinder & Francis Advanced Quant. Mech. (one term) A. Francis Physical Chemistry Lab (half term) R. Sharp UM-Flint: Remedial Chemistry Lecture and Lab with support staff ----Publications---- 1. L. L. Lohr and R. C. Boehm J. Phys. Chem. v.91 p.3203 (1987) "Ab Initio Study of the Gaseous Oxyacids of Phosphorus, Their Conjugate Bases, and Their Corresponding Neutral Radicals" 2. R. C. Boehm and L. L. Lohr J. Phys. Chem. v.93 p.3430 (1989) "An Ab Initio Characterization of Nitrogen Trioxide Electronic States" 3. R. C. Boehm and L. L. Lohr J. Comp. Chem. v.12 p.119 (1991) "Ab Initio Characterization of Several States of Nitroxylium (NO3+): Comparison of Fragmentation Energies of Nitroxylium, Nitroxyl (NO3), and Nitrate" 4. R. C. Boehm and J. L. Gland J. Chem. Ed. v.68 p.455 (1991) "Using Exams to Teach Chemistry More Effectively" 5. R. C. Boehm and A. Banerjee J. Chem. Phys. v.96 p.1150 (1992) "Theoretical Study of Lithium Intercalated Graphite" 6. R. C. Boehm and A. Banerjee Chem. Phys. (accepted) "Ab Initio Study of the Oxides of Rhenium and Their Anions" 7. R. C. Boehm and A. Banerjee Mater. Charact. (submitted) "Ab Initio Study Of Void Stabilization: Oxygen in Nickel" 8. E.E. Hume, R.C. Boehm, M.D. Burrage, S.C. Solomon & V.J. Abreu "Observations and Modeling of the 5577A Dayglow" From chemistry-request@ccl.net Thu Jul 9 21:50:46 1992 Date: Thu, 9 Jul 92 10:54:36 -0400 From: nobody@Kodak.COM Subject: RE:FF repository. To: "chemistry@ccl.net"@Kodak.COM Status: R >From: NAME: Adi M. Treasurywala FUNC: Biophys. & Compu. Chem. TEL: (518)445-7042 To: "chemistry@ccl.net"@kodakr@mrgate@wpc In general I am in favour of anything that makes computational results SCIENTIFIC in the sense of reproducible. This suggestion would appear to do that in some way. May I also add that the complete definition of a FF will also necessitate some clear ref to the optimzer implimentation used. This is usually standard but I have come across some exceptions recently. Finally some commercial software vendors have published calibrations of their force fields and this is a useful step in this direction too. I don't think that one action obviates the other. I would advocate doing BOTH. Adi Treasurywala (adit@kodak.com) From chemistry-request@ccl.net Thu Jul 9 22:43:53 1992 Date: Thu, 9 Jul 92 19:00:11 -0400 From: gallion@auriga.rose.brandeis.EDU (steve gallion) Subject: Angelo Vedani To: CHEMISTRY@ccl.net Status: R ------------------------------------------------------------------------------ For those interested in contacting Angelo Vedani. My latest information is: Angelo Vedani Aeschstrasse 14 CH-4107 Ettingen Switzerland Phone: +41-61-7218958 FAX: +41-1-558010 e-mail: vedani@czheth5a.bitnet Steve Gallion (gallion@auriga.rose.brandeis.edu) ------------------------------------------------------------------------------ From chemistry-request@ccl.net Fri Jul 10 00:27:31 1992 Date: Fri, 10 Jul 92 11:18:57 +1000 From: Tim Astley Subject: Overlap Integrals To: CHEMISTRY@ccl.net Status: R Does anyone out there have access to a programme that calculates diatomic overlap integrals? I'd dearly love to have a copy of one or purchase one etc. It is going to be helpful for my research! :) Any info will be gleefully accepted, Thanks, Tim