From harbowy@chemres.tn.cornell.edu Wed Feb 10 20:06:01 1993 Message-Id: <199302110608.AA02624@oscsunb.ccl.net> From: m.e. Subject: more of the ongoing saga of MOPAC and CI To: CHEMISTRY@ccl.net (computational chemists) Date: Thu, 11 Feb 93 1:06:01 EST Organization: Cornell Chem Grad Student Special thanks to J. Stewart and A. Holder for their time: I have learned much and probably wouldn't be nearly as far along as I am if it were not for them. Here's the new problem. I've been playing with the MICROS=n keyword. Problem is, it won't play back. Period. On mopac 5 as compiled by the cornell theory center, or mopac 6 as compiled by me. It keeps giving an 'end of file reached' file io error on my mopac 6 version. Has anyone successfully used this keyword recently, especially at the Cornell Theory Center (CNSF)? I'm wondering if there's a mistake in my code, or if i'm just not getting it. -- matt ----------------------------------------------------------------------------- |/ _ /\ Matthew Harbowy (ikf@lithium.tn.cornell.edu) |\ - /__\ "I'm the bear that went over the mountain" ----------------------------------------------------------------------------- What kind of rule Can overthrow a fool and leave the land with no stain? -Suzanne Vega From dave@carbon.chem.csiro.au Thu Feb 11 12:31:27 1993 Message-Id: <199302110631.AA02809@shark.mel.dit.csiro.au> Date: Thu, 11 Feb 93 17:31:27 EST From: (Dr.) Dave Winkler Subject: Neural network software for molecular design To: chminf-l@iubvm.ucs.indiana.edu, chemistry@ccl.net Dear Netters, Does anyone know of Neural Network package(s), commercial or otherwise, which can do cross validation and splitting of training data files for the back propagation algorithm? A Macintosh version is preferred with SGI second choice. I have an old version of DartNet from Dartmouth College (which is not supported any more) and NeuralWorks Explorer, neither of which can do what I need. If there are sufficient replies I'll summarize for the net. Thanks, Dave __________________________________________________________________________ Dr. David A. Winkler Voice: 61-3-542-2244 Principal Research Scientist Fax: 61-3-543-8160 CSIRO Division of Chemicals and Polymers Private Bag 10 Clayton, Australia. "Life is what happens to you while you're making other plans" From Leif.Laaksonen@csc.fi Thu Feb 11 11:52:32 1993 Date: Thu, 11 Feb 1993 09:52:32 +0200 Message-Id: <199302110752.AA07173@csc.fi> To: amber@cgl.ucsf.edu, charmm-bbs@emperor.harvard.edu, gromos@igc.ethz.ch, From: Leif.Laaksonen@csc.fi Subject: SCARECROW Computing Presents SCARECROW is a program for the analysis of MD trajectories. It has been published in the J. Mol. Graph. 10 (1992) 33. In fact the program is much more than just a MD analysis package. The package also contains: (1) The ICON8 extended Huckel program modified to eat 1000 atoms. There is an interface from SCARECROW to ICON8. The ICON8 program can generate the input to an electrostatic potential program (VSS). (2) The electrostatic potentiall program VSS. This is a c-code version of the old VSS program. The out put from VSS can be displayed with SCARECROW (3) A probe surface program to generate Connolly type of surfaces. (4) A program to generate orbitals or electron density data from orbitals generated with ICON8. SCARECROW is now able to read several different types of coordinate files like the CHARMM, INSIGHT, PDB and several other types of files. Trajectory analysis can be done for CHARMM, DISCOVER, YASP, MUMOD, GROMOS, and AMBER binary trajectories, and very soon also for HyperChem. Some of the goodies are only available for CHARMM users. New features in SCARECROW are the possibility to calculate radial distribution functions, power spectrum for main component analysis of time series and a possibility to calculate diffusion coefficients and much more. There is a very crude 2D display facility but the data can always be exported to your favourite plotting package. SCARECROW has a graphics interface and runs now only on Silicon Graphics Machines. On SGI machines it's also possible to run SCARECROW without graphics. I don't have any plans to port the stuff to other platforms, sorry. If you are interested to get more information about SCARECROW please feel free to get in touch. I have so far been distributing the program for free, if somebody makes money out of it I want to get my share. Cheers, -leif laaksonen --------------------------------------------------------- Leif.Laaksonen@csc.fi Center for Scientific Computing P.O. Box 405 FIN-02101 Espoo FINLAND Phone: 358 0 4572378 Telefax: 358 0 4572302 Voice Mail: 358 486257407 "In every job to be done there is an element of fun" Mary Poppins --------------------------------------------------------- From OLIVER@psipsy.uct.ac.za Thu Feb 11 06:26:02 1993 Message-Id: To: chemistry@ccl.net From: "Oliver Hill" Date: 11 Feb 93 12:45:25 SAST-2 Subject: Re: ZINDO program > To: CHEMISTRY@ccl.net > Subject: ZINDO program > Cc: ilya@lisboa.ks.uiuc.edu > Sender: chemistry-request@ccl.net > Errors-To: owner-chemistry@ccl.net > Precedence: bulk > > I would like to get the quantum chemistry program ZINDO for the spectra > calculations. I intend to run it on SGI, NEXT, or Cray platform. Does anybody know > how I can get it? Any response will be very much appreciated. > > Ilya Logunov > The ZINDO program is obtainable from Prof. Zerner's group. The person to contact is Dr. Rajiv D. Bendale his E-mail address is : bendale@qtp.ufl.edu The academic code is free, however he told me that there should be a commercial version avalible soon with fancy interface etc. Hope this helps Oliver ______________________________________________________________________ Oliver Hill Department of Chemistry University of Cape Town Rondebosch, 7700 SOUTH AFRICA OLIVER@PSIPSY.UCT.AC.ZA (internet) Tel. +27-21-650-2527 Fax. +27-21-650-3788 ______________________________________________________________________ From schettle@chemix.mpi-stuttgart.mpg.de Thu Feb 11 14:06:18 1993 Date: 11 Feb 1993 13:06:18 +0100 From: schettle@chemix.mpi-stuttgart.mpg.de Subject: Mac summery To: Chemistry@ccl.net Message-Id: <9302111206.AA16047@chemix.mpi-stuttgart.mpg.de> A couple of days ago I asked for special Mac software. Thanks to everybody answered. This is a short review of all answers. 1. question: 3D figures in non-cartesian coordinate system Mathematica proposed by Tom from Strasbourg was already considered by me. I was also looking for alternatives in the very special case of ternary phase diagrams. And indeed there is one program called TCONTOUR by John Pilling. Many thanks to Davide from Milano for this information. 2. question: data analysis and presentation * IGOR from wavemetrics was proposed by Rutger from New Jersey. * DeltaGraphPro from DeltaPoint Inc. was proposed by Kirk from Richland and by Stefan from Hamburg. * CricketGraph from Cricket Software was proposed by Mark Zottola. According to Robert from Carbondale there should be still one advantage of Kaleidagraph, because neither DeltaGraphPro nor CricketGraph have a formula processor, which is indeed extremely useful. Heike Heike Schettler Phone: xx49 - 711 - 686 0 664 MPI-FKF Fax: xx49 - 711 - 687 4 371 Heisenbergstr. 1 email: schettle@chemix.mpi-stuttgart.mpg.de D-7000 Stuttgart 80 From theresa@si.fi.ameslab.gov Thu Feb 11 03:02:29 1993 From: theresa@si.fi.ameslab.gov (Theresa Windus) Message-Id: <9302111502.AA45532@si.fi.ameslab.gov> Subject: Parallel Software To: chemistry@ccl.net () Date: Thu, 11 Feb 93 9:02:29 CST Hello! While GAMESS (the Iowa State University version) is not technically "commercial", we are currently running in parallel on many different platforms. It will run parallel on UNIX workstation clusters (even workstations of different vendors) and several "true" parallel machines (such as the iPSC, Delta, CM-5, etc). We currently accomplish this through the use of the TCGMSG package by Robert Harrison at PNL. We are working on a conversion to PVM from Oak Ridge. If you have a specific machine you have questions about, please feel free to contact me. If you would like a copy of GAMESS, please contact Mike Schmidt at mike@si.fi.ameslab.gov. Theresa Windus Department of Chemistry Iowa State University Ames, IA 50011 e-mail: theresa@si.fi.ameslab.gov From feng@lisboa.ks.uiuc.edu Thu Feb 11 00:13:08 1993 From: Zhou Feng Message-Id: <9302111618.AA16050@lisboa.ks.uiuc.edu> Date: Thu, 11 Feb 93 08:13:08 -0800 To: CHEMISTRY@ccl.net Subject: SCARECROW Leif wrote: ---------------------------------------------------------------------------------------------------------------- SCARECROW is a program for the analysis of MD trajectories. It has been published in the J. Mol. Graph. 10 (1992) 33. In fact the program is much more than just a MD analysis package. The package also contains: (1) The ICON8 extended Huckel program modified to eat 1000 atoms. There is an interface from SCARECROW to ICON8. The ICON8 program can generate the input to an electrostatic potential program (VSS). (2) The electrostatic potentiall program VSS. This is a c-code version of the old VSS program. The out put from VSS can be displayed with SCARECROW (3) A probe surface program to generate Connolly type of surfaces. (4) A program to generate orbitals or electron density data from orbitals generated with ICON8. SCARECROW is now able to read several different types of coordinate files like the CHARMM, INSIGHT, PDB and several other types of files. Trajectory analysis can be done for CHARMM, DISCOVER, YASP, MUMOD, GROMOS, and AMBER binary trajectories, and very soon also for HyperChem. Some of the goodies are only available for CHARMM users. New features in SCARECROW are the possibility to calculate radial distribution functions, power spectrum for main component analysis of time series and a possibility to calculate diffusion coefficients and much more. There is a very crude 2D display facility but the data can always be exported to your favourite plotting package. SCARECROW has a graphics interface and runs now only on Silicon Graphics Machines. On SGI machines it's also possible to run SCARECROW without graphics. I don't have any plans to port the stuff to other platforms, sorry. If you are interested to get more information about SCARECROW please feel free to get in touch. I have so far been distributing the program for free, if somebody makes money out of it I want to get my share. Cheers, -leif laaksonen --------------------------------------------------------- Leif.Laaksonen@csc.fi Center for Scientific Computing P.O. Box 405 FIN-02101 Espoo FINLAND Phone: 358 0 4572378 Telefax: 358 0 4572302 Voice Mail: 358 486257407 "In every job to be done there is an element of fun" Mary Poppins --------------------------------------------------------- --- Administrivia: This message is automatically appended by the mail exploder: CHEMISTRY@ccl.net --- everyone CHEMISTRY-REQUEST@ccl.net --- coordinator OSCPOST@ccl.net send help from chemistry Anon. ftp www.ccl.net CHEMISTRY-SEARCH@ccl.net --- search the archives, read help.search file first --- ------------------------------------------------------------------------------------------------------------------ A few questions: 1. Many of the functions such as trajectory display, power spectrum or radial distribution functions are also available in programs like QUANTA or XPLOR, how is SCARECROW different? 2. Does the electrostatic program include solvation effects by solving Posson-Boltzman equation, or is it just a eletrostatic calculation in vaccum? Feng Zhou From Shahul.Nilar@BRI.NRC.CA Thu Feb 11 07:07:12 1993 Message-Id: <9302111707.AA21144@bobino.BRI.NRC.CA> Date: Thu, 11 Feb 93 12:07:12 -0500 From: Shahul.Nilar@bri.nrc.ca (Shahul Nilar) To: chemistry@ccl.net Subject: conference Does anyone have any information on the American Theoretical Chemistry Conference tobe held in Rochester, i.e. dates, contact person etc. Thanks Shah Nilar From DSMITH@uoft02.utoledo.edu Thu Feb 11 06:31:18 1993 Date: Thu, 11 Feb 1993 11:31:18 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: scaled frequencies for S and H To: chemistry@ccl.net Message-Id: <01GULDUJBASI000PM8@UOFT02.UTOLEDO.EDU> Leif Haldor writes: >You have to scale the frequencies you get from Gaussian by about 0.9. >The enthalphy, entropy and ZPE among other thermodynamical properties >calculated by Gaussian depend upon the frequencies. Does someone on this >list know how you can compute the thermodynamical properties using scaled >frequencies in Gaussian? Probably not possible? If so, has someone written >a program to extract the frequencies from the outputfile or chk-file, >correct for the scaling and then compute the thermodynamical properties? >Or do I have to use Lotus 1-2-3 or Excel after looking up the litterature >references for all the formulas. Robert Topper responds: >You can certainly estimate thermochemical properties from the frequencies >you get from Gaussian. However, you will have to use the rigid-rotator/ >harmonic oscillator (RRHO) approximation to the partition function, which >requires the three principal moments of inertia as well as the >harmonic frequencies. These can be calculated from the molecular >geometry and masses. Also, the calculation may only >be semi-quantitative, unless you have a fancy way of estimating the >partition function. (Significantly more and detailed information has been deleted from this response - DAS.) In a recent manuscript we wrote: "Each HF/6-31G* optimization, and for the monomers the MP2/6-31G* optimizations, were followed by normal frequency analysis to make sure an energy minimum was obtained and for calculating free energies at 298 K and one atmosphere. In the free energy calculations the thermal correction to the enthalpy, H(T) and entropy, S(T) were calculated in the rigid rotor, harmonic oscillator approximation. Ideal gas behavior was accepted in the imidazole protonation reaction and for the formation of monohydrates. The thermal energy contributions were calculated using classical statistical thermodynamic functions. The total entropy for PyW(pi) and Im(3)W without any molecular symmetry contain a term of RTln2 due to the entropy of mixing." Taken from: Nagy, P. I.; Durant, G. J.; Smith, D. A. "Theoretical Studies on Hydration of Pyrrole, Imidazole and Protonated Imidazole in the Gas Phase and Aqueous Solution," J. Am. Chem. Soc., in press. Doug Douglas A. Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu From krystek@alcor.bms.com Thu Feb 11 09:08:29 1993 Date: 11 Feb 1993 14:08:29 -0500 From: krystek@alcor.bms.com (Stanley Krystek) Subject: mac graphics To: chemistry@ccl.net Message-Id: <9302111908.AA23909@alcor.bms.com> I know this has been discussed before, but i was not paying attention. Could someone point me to references for MAC programs that can be used to view protein structures. Thanks in advance. stan Stanley R. Krystek, Jr., Ph.D. Bristol-Myers Squibb Pharmaceutical Research Institute Department of Macromolecular Modeling P.O. Box 4000, Room H.3812, Princeton, N.J. 08543-4000 (609) 252-4100 FAX: (609) 252-6030 INTERNET: krystek@bms.com From DSMITH@uoft02.utoledo.edu Thu Feb 11 08:38:29 1993 Date: Thu, 11 Feb 1993 13:38:29 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: summary of parallel responses To: chemistry@ccl.net Message-Id: <01GULIJO9DKY000PM8@UOFT02.UTOLEDO.EDU> From: IN%"mckelvey@Kodak.COM" 10-FEB-1993 09:26:35.90 how about HONDO from IBM? GAMESS? both run parallel across network. PVM for HONDO and TCGMSG for GAMESS. J McKelevey =========== From: IN%"larryg@AVS.COM" 10-FEB-1993 09:51:34.87 Dear Dr. Smith, Thank you for your interest in AVS. We just implemented a new campus (educational) pricing program whose details I am not completely familiar with, so I'll refrain from speculating on what the price is. I believe that it USED to be a 45% educational discount on top of a single-license price of $6500, but I believe that the new campus pricing program can bring the price way down. The person who DOES know all the pricing details is the salesperson for your area, Bill Lenk. He can be reached at 708-717-8410 or lenk@avs.com. I will also transfer your information to him. As for your questions regarding parallelism on the SGI, we can take advantage of parallelism in two ways: individual modules can be compiled to be run across parallel processors and AVS can be instructed to run different module groups in parallel on different processors. I don't know if your are familiar with the way AVS networks work - we decompose an application into distinct processing tasks (called modules) whose interconnectivity is specified using a graphical network editor. Modules (which can reside in the same UNIX process, different processes, or even different machines) which are 'sibling' modules (those that don't have scheduling dependencies on each other) can be run in parallel: Module A ________|________ | | Module B Module C |________________| | Module D Modules B and C can be run in parallel, but (generally) Module D will not execute unti both B and C are finished. In addition, any of the modules can be compiled to be a parallel. One downside to this is that none of the AVS modules delivered with the system (there are about 200 of them) are compiled to run in parallel. One up side is that there are about 600 modules available as free, public domain modules with source code from the International AVS Center at the North Carolina Supercomputing Center. Anyways, I don't know how much of this you already know. I will try to get Bill Lenk to contact you, but feel free to write or call me with any technical questions you might have. larryg ====================================================================== Larry Gelberg larryg@avs.com Advanced Visual Systems Inc. (AVS Inc.) 300 Fifth Ave. Waltham, MA 02154 Tel: 617-890-4300 Fax: 617-890-8287 ====================================================================== From: IN%"theresa@si.fi.ameslab.gov" 10-FEB-1993 10:47:36.23 Hello! While GAMESS (the Iowa State University version) is not technically "commercial", we are current running in parallel on many different platforms. It will run parallel in UNIX workstation clusters (even workstations of different vendors) and several "true" parallel machines (such as the iPSC, Delta, NCUBE, CM-5, etc). We currently accomplish this through the use of the TCGMSG package by Robert Harrison at PNL. We are working on a conversion to PVM from Oak Ridge. If you have a specific machine you have questions about, please feel free to contact me. If you would like a copy of GAMESS, please contact Mike Schmidt at mike@si.fi.ameslab.gov. Theresa Windus Department of Chemistry Iowa State University Ames, IA 50011 e-mail: theresa@si.fi.ameslab.gov ========== From: IN%"rick@biosym.com" 10-FEB-1993 11:00:19.25 The Discover program from Biosym has been running in parallel on SGI machines for over 3 years. In addition it runs parallel on Alliant, Convex and Cray platforms. Rick Lapp Biosym Technologies, Inc. email: rick@biosym.com ========== From: IN%"jle@world.std.com" 10-FEB-1993 11:12:46.71 I know Gaussian's running in parallel (thanks to Roberto), and Spartan has a parallel Direct SCF for SGI. Martin Guest of Daresbury Labs, UK has a parallel Gamess (GAMESS-UK) if I recall, and several of the govt labs (DOE?) have done work in that area. Mark Murcko at Vertex had Discover built in parallel, but I can't recall the speedup. There's always the question of throughput vs. single-job speed... Also, folks "forgot" and submitted several full-paralllel jobs on the machine(s), which REALLY slowed things down. Since there's still little/no software to help parallelize things, I don't think there's been much progress. Joe ========== From: IN%"bbesler@ouchem.chem.oakland.edu" 10-FEB-1993 11:29:13.60 Gaussian 92C is optimized to take advantage of the symmetric multuple processing capabilities of the SGI's. I am not sure about the multiprocessor R4000 systems. I don't SGI has "officially" announced the yet. ========== From: IN%"bernhold@qtp.ufl.edu" 10-FEB-1993 11:55:01.31 Under SunOS 4.1, multi-CPU Suns don't have any facilities for the sort of programming you want. Parallelism occurs at the process level -- there is no way to find out what processor you are running on, nor any way to control it. If you had very coarse-grained parallelism, you could spawn (say) four processes, but ther is not way to guarantee they would actually run in parallel -- it would depend on load. Of course if you have the machine to yourself, it is _likely_ they'll run in parallel... I don't know if this changes in SunOS5 (Solaris 2.x), but I don't really think so. -- David Bernholdt bernhold@qtp.ufl.edu Quantum Theory Project bernhold@ufpine.bitnet University of Florida Gainesville, FL 32611 904/392 6365 =========== From: IN%"dzung@biosym.com" 10-FEB-1993 12:45:35.90 Biosym molecular mechanics and dynamics program DISCOVER is ported to the nCube2 and the KSR1. We are working on the MPP version of our Density Functional codes DMol and deMon. Dzung ============================================================= Dzung T. Nguyen,Ph.D. (e-mail: dzung@biosym.com) Biosym Technologies, Inc. Phone: (619) 546-5313 9685 Scranton Road Fax: (619) 458-0136 San Diego, CA 92121-2777 ============================================================= From: IN%"hyper!burton@autodesk.com" 10-FEB-1993 18:40:06.67 >Is Hyperchem going to run in parallel on the recently announced SGI machines? > >Doug > Dr. Smith, We already do. In response to your inquiry, the SGI Workstation release of HyperChem already does take advantage of multiple processors. In this release, there is a Communications... option in the Setup menu, which allows the user to specify the number of nodes which the computation will be distributed over, as well as specify whether the computation will be performed on the local or a remote host. After the number of nodes is specified, the kernel then is responsible for distributing these over multiple processors. If the number of nodes exceeds the number of processors, then the kernel may emulate multiple processes, but these will not be running in parallel. This should not change for the new SGI series of workstations. In release 2.0 of the SGI Workstation version of HyperChem Extended Huckel, CNDO, INDO, MINDO/3, MNDO, AM1, PM3, AMBER, BIO+ and OPLS methods all have the ability to run on parallel processors. Cheers. Ian. -- Ian Burton Hypercube, Inc. Internet: burton@hyper.com #7-419 Phillip St. Telephone: (519) 725-4040 Waterloo, Ontario Facsimile: (519) 725-5193 Canada N2L 3X2 ========== From: IN%"theresa@si.fi.ameslab.gov" 11-FEB-1993 09:53:47.89 Hi! Parallel GAMESS should work on a parallel Alliant, but we have not tested this recently. If you have any trouble, please let me know. Theresa Department of Chemistry Iowa State University Ames, IA 50011 e-mail: theresa@si.fi.ameslab.gov From chs1nt@surrey.ac.uk Thu Feb 11 18:21:46 1993 From: Dr Nicholas P Tomkinson Message-Id: <9302111821.AA23452@central.surrey.ac.uk> Subject: IBM vs. SGI To: chemistry@ccl.net Date: Thu, 11 Feb 93 18:21:46 GMT Dear All, Here at Surrey we are intending to buy a major commercial computational chemistry package that will run on either IBM or SGI platforms. I have a bias towards SGI, but IBM are cheaper. Leif Laaksonen recently posted an article about SCARECROW in which he specifies SGI as the only platform he has written for. Most comp. chem. software will run on SGI or is in the process of being ported to SGI. Is it the case, as is my feeling, that IBM is not yet supported to the same extent by the community? Would we be restricting ourselves by buying IBM rather than SGI, or is it trivial to port from SGI to IBM - are there minor but irritating incompatibilites? All responses are appreciated - if there is enough response I will summarise to the list. Nick Tomkinson From h8714031@hkuxa.hku.hk Thu Feb 11 21:26:04 1993 Date: Fri, 12 Feb 93 10:09:35 WST From: h8714031%hkuxa.hku.hk@OHSTVMA.ACS.OHIO-STATE.EDU Subject: MO Plotting program! To: CHEMISTRY@ccl.net Message-Id: <9302120209.AA08613@hkux2.hku.hk> Dear Netters, I am looking for a program that can plot the MO graphically. I am using GAMESS. There is a program pltorb that can plot the MO on X-windows and postscript. I want to know whether there is a package that can plot the MO in 3D. Thanks in advance!!! K.W.Mok Email h8714031@hkuxa.hku.hk