From zhuming@igd.fhg.de Wed Apr 15 05:24:41 1998 Received: from monster.igd.fhg.de for zhuming@igd.fhg.de by www.ccl.net (8.8.3/950822.1) id EAA28219; Wed, 15 Apr 1998 04:26:29 -0400 (EDT) Received: from tizian.igd.fhg.de by monster.igd.fhg.de (5.x/SMI-4.1) id AA24356; Wed, 15 Apr 1998 10:25:15 +0200 Received: by tizian.igd.fhg.de (950413.SGI.8.6.12/SMI-4.0) id KAA19784; Wed, 15 Apr 1998 10:25:14 +0200 To: chemistry@www.ccl.net Subject: Cooperation Opportunity: Virtual Reality Molecular Modeling Return-Receipt-To: zhuming@igd.fhg.de X-Face: VhKTO2~@KRKIn"ETN@zEOT8VHo"ijQ<6Oq& Date: 15 Apr 1998 10:25:14 +0200 Message-Id: Lines: 47 X-Mailer: Gnus v5.5/XEmacs 20.4 - "Emerald" Offer for free access to a prototype Virtual Reality Molecular Modeling system -------------------------------------------------------------- This is for providing a cooperation opportunity for chemists or biochemists who are working on molecular modeling or drug design to use the most state-of-the-art Molecular Modeling in Virtual Environment technique available today. At Fraunhofer Institute for Computer Graphics we have developed a virtual environment, RealMol, for interactive molecular modeling and molecular dynamics simulation. The CAVE (a highly sophisticated five-sided VR stereo projection system) or head mounted display and a cyberglove are used for immersive display and interaction with the molecular system. A molecular dynamics simulation program (NAMD) is linked to the virtual environment to simulate the physical and chemical properties of the molecular system in real-time. A high-speed network exchanges data between the simulation program and the modeling program. This virtual environment provides scientists with a powerful tool to study immersively the world of molecules and is very helpful in the fields like rational drug design. We are looking for scientists who want to solve their real-world problem using a virtual environment. Our goal is to evaluate the present system and to identify achievements as well as future directions of research in this field. If you are interested in working with your own data in our CAVE in Darmstadt, Germany, please contact us. Currently our program can read molecular coordinate data in PDB format, and dynamics simulation trajectories in X-PLOR's DCD format. Your participation is free of charge - publication of the results is intended, but of course the matter will be treated confidential if wished. Details about our project can be found at: http://www.igd.fhg.de/www/igd-a4/research/chemie/ Point of contact: Zhuming Ai, Torsten Fr=F6hlich, Helmut Haase Fraunhofer Institute for Computer Graphics Rundeturmstr. 6 64283 Darmstadt Germany Fax: +49-6151-155 196 e-Mail: zhuming@igd.fhg.de From citra@syrres.com Wed Apr 15 09:24:44 1998 Received: from apollo.syrres.com for citra@syrres.com by www.ccl.net (8.8.3/950822.1) id JAA29408; Wed, 15 Apr 1998 09:03:20 -0400 (EDT) Received: from pc-citra.syrres.com ([204.168.121.167]) by apollo.syrres.com (Netscape Mail Server v2.0) with SMTP id AAA201 for ; Wed, 15 Apr 1998 09:02:29 -0400 X-Sender: citra@srcinet.syrres.com X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: citra@syrres.com (mario citra) Subject: Radius of hydrated ions Date: Wed, 15 Apr 1998 09:02:29 -0400 Message-ID: <19980415130229348.AAA201@pc-citra.syrres.com> Can anyone point me to some general information on how to estimate the radius of hydrated ions? ********************************** * Regards, * * Mario J. Citra PhD * * Syracuse Research Corporation * * 6225 Running Ridge Road * * North Syracuse, New York 13212 * * * * phone 315-452-8406 * * email citra@syrres.com * ********************************** From ppang426@netvigator.com Wed Apr 15 10:24:44 1998 Received: from imsp073.netvigator.com for ppang426@netvigator.com by www.ccl.net (8.8.3/950822.1) id JAA29917; Wed, 15 Apr 1998 09:24:50 -0400 (EDT) Received: from patrick (hhtam011141.netvigator.com [208.139.102.141]) by imsp073.netvigator.com (8.8.8/8.8.8) with SMTP id VAA14362 for ; Wed, 15 Apr 1998 21:24:06 +0800 (HKT) Message-ID: <3534B676.267@netvigator.com> Date: Wed, 15 Apr 1998 21:30:30 +0800 From: Patrick Reply-To: ppang426@netvigator.com Organization: Chemistry X-Mailer: Mozilla 3.01C-IMS (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: rotational speed of small molecule in water medium Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello! Have you any idea about the rotational speed of small molecule in water medium? Here, the small molecule is defined as the diameter is small than 12 angstroms if the small molecule is assumed as a sphere. Thank you for your attention. Pang From eugene@liposome.genebee.msu.su Wed Apr 15 10:43:41 1998 Received: from liposome.genebee.msu.su for eugene@liposome.genebee.msu.su by www.ccl.net (8.8.3/950822.1) id JAA00065; Wed, 15 Apr 1998 09:51:58 -0400 (EDT) Received: (from eugene@localhost) by liposome.genebee.msu.su (8.8.5/8.8.5) id RAA03099; Wed, 15 Apr 1998 17:51:49 +0400 From: Eugene Leitl MIME-Version: 1.0 Content-Type: message/rfc822 Content-Transfer-Encoding: 7bit Date: Wed, 15 Apr 1998 17:51:49 +0400 (MSD) To: chemistry@www.ccl.net Subject: FYI: Some ScaLAPACK performance numbers on Beowulf X-Mailer: VM 6.43 under 20.4 "Emerald" XEmacs Lucid Message-ID: <13620.47959.324772.230779@liposome.genebee.msu.su> Return-Path: Received: from cesdis.gsfc.nasa.gov (cesdis1.gsfc.nasa.gov [128.183.38.12]) by liposome.genebee.msu.su (8.8.5/8.8.5) with SMTP id EAA15377 for ; Wed, 15 Apr 1998 04:18:32 +0400 Received: by cesdis.gsfc.nasa.gov (4.1/SMI-4.1) id AA08879; Tue, 14 Apr 98 19:44:44 EDT Received: from eis-msg-012.jpl.nasa.gov by cesdis.gsfc.nasa.gov (4.1/SMI-4.1) id AA08873; Tue, 14 Apr 98 19:44:11 EDT Received: from volcanoes.jpl.nasa.gov by eis-msg-012.jpl.nasa.gov; Tue, 14 Apr 1998 16:52:25 -0700 Received: by volcanoes.Jpl.Nasa.Gov (SMI-8.6/SMI-SVR4) id QAA28753; Tue, 14 Apr 1998 16:54:15 -0700 Message-Id: <199804142354.QAA28753@volcanoes.Jpl.Nasa.Gov> X-Sun-Charset: US-ASCII Precedence: bulk From: Paul.L.Springer@jpl.nasa.gov (Paul Springer) Sender: owner-beowulf@cesdis1.gsfc.nasa.gov To: beowulf@cesdis1.gsfc.nasa.gov Subject: Some ScaLAPACK performance numbers on Beowulf Date: Tue, 14 Apr 1998 16:54:15 -0700 Using the ASCI BLAS package on a Beowulf with ScaLAPACK, I got some pretty reasonable numbers for multiplying two matrices of double precision numbers. In the table below, N is the order of each (square) matrix: N 1000 2000 4000 8000 ------------------------------------- node config| -----------| 2x2 | 276 436 396 4x4 | 285 742 1256 1329 Units are in MFlop/s. The nodes are 200 MHz Pentium Pro's running Linux. The BLACS layer under ScaLAPACK was PVM based. But it had to be modified to call PVM with the PvmDirectRoute option. Without this modification performance figures are cut in half. Performance drops in the 2x2 configuration probably because the block size had to be decreased to 100 because of memory limitations. On all other runs the block size was N/2 for the 2x2 case and N/4 for the 4x4 case. Exception: for the case where N = 8000, the block size also had to be decreased to 100. Paul Springer ------------------ Paul Springer High Performance Computing Group Jet Propulsion Laboratory pls@jpl.nasa.gov From barna@jedlik.phy.bme.hu Wed Apr 15 11:24:52 1998 Received: from jedlik.phy.bme.hu for barna@jedlik.phy.bme.hu by www.ccl.net (8.8.3/950822.1) id KAA00244; Wed, 15 Apr 1998 10:25:38 -0400 (EDT) Received: from localhost (barna@localhost) by jedlik.phy.bme.hu (8.8.5/8.8.5) with SMTP id QAA02070 for ; Wed, 15 Apr 1998 16:27:46 +0200 Date: Wed, 15 Apr 1998 16:27:45 +0200 (MET DST) From: Barna Imre To: chemistry@www.ccl.net Subject: Core Potential for Silicon Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Sir, At first I would like to apologize for disturbing. I am a Phd. Student and looking for potentials for silicon. What kind of potentials (Morse, spring ?) are used in bulk silicon ? What are the parameters ? Thank You for any kind of help. Best Regards, Imre Barna From genghis@darkwing.uoregon.edu Wed Apr 15 11:57:41 1998 Received: from darkwing.uoregon.edu for genghis@darkwing.uoregon.edu by www.ccl.net (8.8.3/950822.1) id KAA00342; Wed, 15 Apr 1998 10:40:59 -0400 (EDT) Received: from localhost (genghis@localhost) by darkwing.uoregon.edu (8.8.8/8.8.8) with SMTP id HAA02465 for ; Wed, 15 Apr 1998 07:40:48 -0700 (PDT) Date: Wed, 15 Apr 1998 07:40:48 -0700 (PDT) From: "Dale A. Braden" Reply-To: "Dale A. Braden" To: cclpost Subject: G94:scf=qc/diis problem Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL, To find a converged DFT wave function for an open-shell anion in a dielectric medium, I had to use the quadratically convergent SCF method. It worked. However, the Gaussian 94 manual seems to suggest that this method is among those that tend to converge to the nearest solution, which might not be a true minimum with respect to orbital rotations. So, once I had the converged SCF=QC solution (which was obtained using SCF=TIGHT), I used it as the initial guess for another single point calculation using the default DIIS method. I could not get this to converge, even by relaxing the convergence criterion, using extra integral accuracy (i.e., using SCF=novaracc but not SCF=tight) or level-shifting. The QC wave function was found to be stable (stable=opt scf=qc). I am simply curious to know why the DIIS method fails so badly when given an already optimized wave function. What property of the system (density matrix? orbital energies?) causes DIIS to be so sensitive that it never converges? Best wishes to all, Dale Braden Department of Chemistry University of Oregon Eugene, OR 97403-1253 genghis@darkwing.uoregon.edu From gdurst@dowagro.com Wed Apr 15 14:24:46 1998 Received: from elinet1.dowagro.com for gdurst@dowagro.com by www.ccl.net (8.8.3/950822.1) id NAA02000; Wed, 15 Apr 1998 13:32:19 -0400 (EDT) Received: by elinet1.dowagro.com id AA01705 (InterLock SMTP Gateway 3.0 for chemistry@www.ccl.net); Wed, 15 Apr 1998 12:32:20 -0500 Received: by elinet1.dowagro.com (Internal Mail Agent-1); Wed, 15 Apr 1998 12:32:20 -0500 Message-Id: From: "Durst, Gregory L." To: "'chemistry@www.ccl.net'" Subject: Neural network software for PC Date: Wed, 15 Apr 1998 12:34:18 -0500 X-Mailer: Microsoft Exchange Server Internet Mail Connector Version 4.0.994.63 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hello CCL, I have been looking into the use of neural networks for QSAR problems and have found a nice shareware program for Windows 95 machines (WinNN32) that I uploaded to the CCL archive. Jan asked that I announce it, so here are the details. The program can be downloaded from: ftp://www.ccl.net/pub/chemistry/software/MS-WIN95-NT/Neural-Networks or the authors page: http://www.geocities.com/SiliconValley/Lab/9052/winnn.html (*there are links to chemistry applications of WinNN on this page) WinNN32 uses a feed-forward, back propagation algorithm that has been commonly used for "regression" type problems where you want to predict a response from input parameters. I have found the program easy to use and relatively quick. Check it out if you are interested. ... for starters a select few QSAR/NN references (3 with datasets) ... T. Aoyama, Y. Suzuki, H. Ichikawa, 'J. Med. Chem.', v33, (1990), 2583-2590. T.A. Andrea and H. Kalayeh, 'J. Med. Chem.', v34, (1991), 2824-2836. S.-S. So and W.G. Richards, 'J. Med. Chem.', v35, (1992), 3201-3207. D.J. Livingstone and D.T. Manallack, 'J. Med. Chem.', v36, (1993), 1295-1297. J.H. Wikel and E.R. Dow, 'Bioorg. Med. Chem. Let.', v3(4), (1993), 645-651. -NN books- J. Zupan and J. Gasteiger, "Neural Networks for Chemists: An Introduction", VCH, Weinheim, 1993. J. DeVillers, "Neural Networks in QSAR and Drug Design", Academic Press, NY, 1996. The usual disclaimer: I'm only pointing out the availability of the WinNN program, all risks of using WinNN and it's results are your own. Regards, Greg +---------------------------------------------------------------------+ | Gregory L. Durst Computational Chemistry | | phone: 317/337-3413 Dow AgroSciences | | email: gdurst@dowagro.com 9330 Zionsville Rd. 306/D2 | | Indianapolis, IN 46268 USA | +---------------------------------------------------------------------+ From seabra@NPD.UFPE.BR Wed Apr 15 15:24:48 1998 Received: from NPD1.NPD.UFPE.BR for seabra@NPD.UFPE.BR by www.ccl.net (8.8.3/950822.1) id OAA02917; Wed, 15 Apr 1998 14:54:51 -0400 (EDT) Received: from danon ([150.161.5.125]) by NPD.UFPE.BR (PMDF V5.1-4 #20469) with SMTP id <01IVWJVYN7HS0002AX@NPD.UFPE.BR> for chemistry@www.ccl.net; Wed, 15 Apr 1998 15:57:29 GMT-3 Date: Wed, 15 Apr 1998 16:04:22 -0300 From: Gustavo de Miranda Seabra Subject: Basis set limitations on GAMESS? To: chemistry@www.ccl.net Reply-to: Gustavo de Miranda Seabra Message-id: <004601bd68a1$4d9e5f50$7d05a196@danon.dqf.ufpe.br> MIME-version: 1.0 X-Mailer: Microsoft Outlook Express 4.72.2106.4 Content-type: text/plain; charset="iso-8859-1" Content-transfer-encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Dear all, I am trying to make some GAMESS calculation about the Li-F when the atoms are very close from each other. I am using the 10s6p (Huzinaga) for the Neon atom scaled by 25% to the fluorine anions and the 14s (Partridge) to the Li+ ions. But GAMESS always gives me the same error message: " *** ERROR, NO MORE THAN 40 GAUSSIANS PER SHELL " Note that I have already tryed to change the default value (it was 30 gaussians), and to change to a smaller basis set, but it has not fixed the problem. It may be interesting to note that I also tryed to maka an F-...F- calculations and it did work! (there are more gaussians than in the LiF case). Does anyone know what can it be? Thanks very much. ---------------------------------------------------------------------------- --------------- Gustavo de Miranda Seabra MSc Student in Chemistry seabra@npd.ufpe.br Federal University of Pernambuco Brazil ---------------------------------------------------------------------------- --------------- From nakiya@engin.umich.edu Wed Apr 15 15:38:36 1998 Received: from phoenix.engin.umich.edu for nakiya@engin.umich.edu by www.ccl.net (8.8.3/950822.1) id OAA02872; Wed, 15 Apr 1998 14:50:59 -0400 (EDT) Received: from localhost (nakiya@localhost [127.0.0.1]) by phoenix.engin.umich.edu (8.8.7/8.8.7) with SMTP id OAA17862 for ; Wed, 15 Apr 1998 14:50:57 -0400 (EDT) Date: Wed, 15 Apr 1998 14:50:56 -0400 (EDT) From: Naoko Akiya Reply-To: Naoko Akiya To: chemistry@www.ccl.net Subject: CCL: MD package - SUMMARY In-Reply-To: <199804131818.PAA04125@dfa.ifi.unicamp.br> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Here is the question I posted a few days ago: > I am looking for an MD package that can do the following: > > - uses user-supplied potential models as well as built-in models > - does isothermal simulation with Nose-Hoover thermostat > - works on Unix, preferably HP > - calculates free energy > - lets the user follow the trajectory of a particular molecule from a > given initial condition > - can do multiple timestep integration > > If you have any suggestions for a particular MD package that does all > or some of the above, please let me know. FYI we are not looking into > polymers or macromolecules. I will summarize the responses if there is > any interest. Here are the replies: ----------------------------------------------------------------- >From Dayong He Try to find the homepage of GROMACS, it is free for academic purpose, has many options: MD, NEMD, energy minimization, .... ----------------------------------------------------------------- >From Simon Hogg You might want to look at TINKER http://dasher.wustl.edu I think it can do all those things, but I'm not a developer, so I'm not 100% sure. ----------------------------------------------------------------- >From Jordi Villa Freixa A good package that allows easy implementation of user-supplied potential models is TINKER. You can found it in: http://dasher.wustl.edu/tinker/ ----------------------------------------------------------------- >From Keith Refson The only program I can think of which will do this is DL_POLY. Info at http://www.dl.ac.uk/CCP/CCP5/dl_poly.html I believe it does nearly everything you want. The exception is to "calculate free energy" which is of course impossible in practice. You can calculate relative free energies of two systems in equilibrium using Gibbs ensemble or Grand Canonical monte Carlo or free energy along a constrained reaction co-ordinate using the potential of mean force method. I can't remember whether DL_POLY can do a PMF calculation or not, but I think it may. My own MD program, moldy does not have PMF, a multiple timestep, nor any "built in" models, but if you look at my web page I have links to other MD codes. http://www.earth.ox.ac.uk/~keith/moldy.html ----------------------------------------------------------------- >From German Sastre Navarro I'm extremelly pleased with DL_POLY which I've been using for diffusion of hydrocarbons in microporous materials. It's a general MD code, extremelly flexible, and can run on a wide variety of machines, with one or many processors. If you're interested contact Dr. Will Smith at Daresbury Laboratory, U.K. : w.smith@dl.ac.uk ----------------------------------------------------------------- Thank you all for your response. After checking all the recommended programs (and others not listed above), however, I have come to a conclusion that none of them do everything I need. (Maybe I just need to collect more information about each program.) So if I do use them I will have to make substantial modifications/additions myself, in which case I may be better off just writing my own code... If anyone thinks otherwise, please let me know. Sincerely, Naoko =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Naoko Akiya nakiya@engin.umich.edu University of Michigan Dept. of Chemical Engineering phone (734) 764-7121 Ann Arbor, MI 48109-2136 fax (734) 763-0459 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=