From chemistry-request@www.ccl.net Wed Mar 10 10:31:25 1999 Received: from hermes.bmc.uu.se (hermes.bmc.uu.se [130.238.39.159]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA13088 Wed, 10 Mar 1999 10:31:24 -0500 (EST) Received: from alpha2.bmc.uu.se ([130.238.37.65]) by hermes.bmc.uu.se (post.office MTA v2.0 0813 ID# 0-17733) with SMTP id AAA9635 for ; Wed, 10 Mar 1999 16:26:24 +0100 Received: from ronja.bmc.uu.se by alpha2.bmc.uu.se; (5.65v3.2/1.1.8.2/30Jan97-1111AM) id AA03770; Wed, 10 Mar 1999 16:31:21 +0100 Date: Wed, 10 Mar 1999 16:31:03 +0100 (W. Europe Standard Time) From: John Marelius Reply-To: John Marelius To: chemistry@www.ccl.net Cc: Karin Kolmodin , Isabella Feierberg Subject: Molecular modelling software in education: recommendations? Message-Id: X-X-Sender: john@alpha2.bmc.uu.se Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL members, I teach a course in molecular and statistical mechanics for third-year biotechnology students. Until now the students have used Insight II from MSI for the computer exercises, but now I am looking into what other software packages could be used. I would appreciate if you would share any experience you have with other packages, particularly in an undergraduate course context. The exercises contain * visualisation of proteins * building small molecules and peptides * energy minimisation * conformational search * molecular dynamics of small molecules and proteins with explicit solvent * free energy perturbation simulations * receptor-ligand docking and scoring I would prefer a package which runs on one or more of MS Windows NT, Linux or Sun Solaris. I will be happy to summarise the responses to the list. regards, John Marelius +-----------------------------------------------------------------+ | John Marelius | | Dept. of Molecular Biology, Uppsala University | | E-mail: John.Marelius@molbio.uu.se | | phone: +46 18 4714988, fax: +46 18 536971 | | address: Box 590, S-751 24 Uppsala, Sweden | +-----------------------------------------------------------------+ From chemistry-request@www.ccl.net Wed Mar 10 11:08:32 1999 Received: from pscuxc.psc.edu (pscuxc.psc.edu [128.182.73.178]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA13584 Wed, 10 Mar 1999 11:08:32 -0500 (EST) Received: from localhost (benv@localhost) by pscuxc.psc.edu (8.8.7/8.8.7/psc) with ESMTP id LAA06953 for ; Wed, 10 Mar 1999 11:08:32 -0500 (EST) Date: Wed, 10 Mar 1999 11:08:31 -0500 (EST) From: "Benjamin B. Vendeland" To: chemistry@www.ccl.net Subject: CCL: Parallel Supercomputing Workshop at Shippensburg Univ Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Pittsburgh Supercomputing Center Supercomputing Techniques PSC will offer a workshop to students and researchers associated with Pennsylvania academic institutions. The workshop is designed for people who have an interest in applying high performance computing to their teaching or research or who are simply interested in knowing more about parallel computing. Location: Shippensburg University Date: May 13-14, 1999 Application deadline: April 26, 1999. PURPOSE: The purpose of this two day workshop is to introduce participants to parallel processing on the CRAY T3E and to explore more advanced topics, including message passing, performance monitoring and optimization techniques. To ensure quality training, our workshops incorporate both lectures and extensive hands-on lab sessions. Our instructors have strong scientific and technical backgrounds and are available for individual consultation during lab sessions. * A working knowledge of FORTRAN or C and UNIX is required. * Parallel computing experience is not necessary. REGISTRATION: Registration fees are waived to students, professors or researchers associated with academic institutions in the state of Pennsylvania. Please complete and return the enclosed registration form by April 26, 1999 to: Workshop Application Committee ATTN: Dr. Marcela Madrid Pittsburgh Supercomputing Center 4400 Fifth Avenue Pittsburgh, PA 15213. You may also apply for this workshop by sending the requested information via electronic mail to workshop@psc.edu or via fax to (412/268-5832). For additional online information, an agenda and lecture notes, please visit the workshop's homepage at http://www.psc.edu/ training/Shipp/welcome.html or contact the workshop coordinator at workshop@psc.edu For on-site information at Shippensburg, please contact Carol A. Wellington, PhD Assistant Professor Shippensburg University cawell@ship.edu From chemistry-request@www.ccl.net Tue Mar 9 00:49:24 1999 Received: from pobox.csc.fi (pobox.csc.fi [128.214.46.62]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id AAA26125 Tue, 9 Mar 1999 00:49:23 -0500 (EST) Received: from laaksonen.csc.fi (laaksonen.csc.fi [193.166.1.75]) by pobox.csc.fi (8.9.0.Beta5/8.9.0.Beta5/CSC/Rtrs-1.22) with ESMTP id HAA08500; Tue, 9 Mar 1999 07:49:18 +0200 (EET) Date: Tue, 9 Mar 1999 07:49:52 +0200 (GTB Standard Time) From: Leif Laaksonen To: "Prof. Robert Topper" cc: chemistry@www.ccl.net Subject: Re: CCL:Re: CCL:QC journals 'in trouble' In-Reply-To: <199903051713.MAA07615@robin.cooper.edu> Message-ID: X-X-Sender: laaksone@laaksonen.csc.fi MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Robert Topper's last message about the outrageously high journal prices was very good endeed. I would recommend you all to read the article by Declan Butler in the vol. 397 21 January 1999 issue of Nature titled "The writing is on the web for science journals in print". Frome the article one can read that the US Association of Research Libraries calculates that its 114 member libraries spend 142 per cent more on journals in 1997 than ten years before, but order 6 per cent fewer titles. The article contains a lot of good statistics and numbers. Then we have also seen the merge of Beilstein and MDL into Elsevier. Other publishers also seem to be interested to move into the end-product market rather than staying in the content segment. As you all must know the publishers are now very rapidly digitizing their journals and supporting their journals also through the net. I know that very many countries, including Finland (http://hul.helsinki.fi/finelib/english), have made agreements on a national basis to offer the journals digitally. This does not of course solve totally the problem with high subscription prices but it might be a way to go. I know this has directly nothing to do with comp. chem. but it still might be interesting. Cheers, -leif laaksonen ------------------------------------------------------------------- Center for Scientific Computing | Phone: 358 9 4572378 P.O. Box 405 | Mobile: 358 400425203 FIN-02101 Espoo | Telefax: 358 9 4572302 FINLAND | Mail: Leif.Laaksonen@csc.fi -------- URL: http://laaksonen.csc.fi/leif.laaksonen.html --------- On Fri, 5 Mar 1999, Prof. Robert Topper wrote: > > Journal subscription prices in the sciences are outrageously > expensive. If you compare our costs to those of the nonscience > journals, it's a crime how much libraries are being charged. > So only the wealthy libraries can afford complete collections... > and they are in effect subsidizing other libraries which borrow > copies of journals they themselves can't afford to buy. > I myself work at an institution which pays a neighboring > university for access to its journals, so that we don't have to > buy them ourselves. Between that access, the New York Public > Library, and the occasional kindness of neighboring universities > like Columbia, Rutgers and Seton Hall, I manage. But it > definitely makes it harder to get work done when you are running > all over the tri-state area just to get a peek at an article. > In that sense, if there were only 3 places to pubish, I guess > > When will this madness end?! When authors and editors revolt > against these ridiculous journal prices! And along those lines, > I'd like to salute the Internet Journal of Chemistry-which is totally > free, maintains high standards, is fully indexed, and serves > the community of theoretical chemistry well (since it's online, > no more mailing preprints!!). I also respect the efforts of > the ACS and APS, which are both nonprofit organizations, to > keep journal prices at reasonable and affordable levels. > > Hoping for a better future for our library resources, > Robert > > > > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- > > From chemistry-request@www.ccl.net Wed Mar 10 13:57:26 1999 Received: from pscuxc.psc.edu (pscuxc.psc.edu [128.182.73.178]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA15609 Wed, 10 Mar 1999 13:57:26 -0500 (EST) Received: from localhost (benv@localhost) by pscuxc.psc.edu (8.8.7/8.8.7/psc) with ESMTP id NAA01042 for ; Wed, 10 Mar 1999 13:57:27 -0500 (EST) Date: Wed, 10 Mar 1999 13:57:27 -0500 (EST) From: "Benjamin B. Vendeland" To: chemistry@www.ccl.net Subject: The Pittsburgh Supercomputing Center will offer a workshop on Single Particle Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Pittsburgh Supercomputing Center Supercomputing Techniques PSC will offer a workshop to students and researchers associated with Pennsylvania academic institutions. The workshop is designed for people who have an interest in applying high performance computing to their teaching or research or who are simply interested in knowing more about parallel computing. Location: Shippensburg University Date: May 13-14, 1999 Application deadline: April 26, 1999. PURPOSE: The purpose of this two day workshop is to introduce participants to parallel processing on the CRAY T3E and to explore more advanced topics, including message passing, performance monitoring and optimization techniques. To ensure quality training, our workshops incorporate both lectures and extensive hands-on lab sessions. Our instructors have strong scientific and technical backgrounds and are available for individual consultation during lab sessions. * A working knowledge of FORTRAN or C and UNIX is required. * Parallel computing experience is not necessary. REGISTRATION: Registration fees are waived to students, professors or researchers associated with academic institutions in the state of Pennsylvania. Please complete and return the enclosed registration form by April 26, 1999 to: Workshop Application Committee ATTN: Dr. Marcela Madrid Pittsburgh Supercomputing Center 4400 Fifth Avenue Pittsburgh, PA 15213. You may also apply for this workshop by sending the requested information via electronic mail to workshop@psc.edu or via fax to (412/268-5832). For additional online information, an agenda and lecture notes, please visit the workshop's homepage at http://www.psc.edu/ training/Shipp/welcome.html or contact the workshop coordinator at workshop@psc.edu For on-site information at Shippensburg, please contact Carol A. Wellington, PhD Assistant Professor Shippensburg University cawell@ship.edu From chemistry-request@www.ccl.net Wed Mar 10 16:31:26 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 QAA23824 Wed, 10 Mar 1999 16:31:26 -0500 (EST) Received: from theory6.chem.pitt.edu (theory6.chem.pitt.edu [136.142.109.81]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id QAA01578 for ; Wed, 10 Mar 1999 16:31:23 -0500 (EST) Received: from localhost (fer@localhost) by theory6.chem.pitt.edu (AIX4.2/UCB 8.7/8.7) with ESMTP id QAA12398 for ; Wed, 10 Mar 1999 16:30:57 -0500 (EST) Date: Wed, 10 Mar 1999 16:30:57 -0500 (EST) From: Fernando Vila To: Computational Chemistry List Subject: Damped Coulomb Potential Summary Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Fellows; I would like to thank all the people that replied to me request. Right after I sent my e-mail to the list I decided to give it a new try. At the very beginning of my equations I found an error that was complicating everything. After I fixed that the integrals turned out to be embarrassingly easy, easier than those including only the Coulomb potential. The references you sent will be useful to double check my results. My original question was: Dear Fellows, For the past weeks I have been trying to calculate the matrix elements for a damped Coulomb potential to no avail. The potential has the form: erf(a|r-R|) V(r) = ------------- |r-R| where r and R are position vectors and erf(t) is the error function: 2 t erf(t) = -------- int exp(-x^2) dx. PI^(1/2) 0 The matrix elements then are of the form: erf(a|r-R|) gij = int gi V(r) gj dr = int ----------------- dr |r-R| Here gi are spherical Gaussians and gij is the resulting Gaussian from the Gaussian Product Theorem. I have tried using techniques similar to those used for the calculation of the pure Coulomb potential (based on Fourier or Laplace transforms) but the usual cancellation is not complete. Any pointers to papers, books or web pages are welcome.. The complete solution is also very much welcome.. :-) Thanks to all in advance, Fer. Here is a summary of the replies I received: ========================================================================== From: koelmel Hi, Lecture Notes in Chemistry, vol. 48, authored by C. Pisani, R. Dovesi and C. Roetti, titled "Hartree-Fock Ab Initio Treatment of Crystalline Systems" (1988, springer) may be a useful reference. What you're looking for is mentioned on page 60. One way is to convert 1/r into an integral using the Laplace transform trick, then change the order of integration, I think. Hope this helps somewhat Cheers, Christoph ========================================================================== From: Frank Jensen Try looking up some of Peter Gill's work in recent years. They have played with screened Coulomb potentials. Frank ========================================================================== From: Norge Cruz Hernandez Hi , Try to see : S. Obara and A. Saika. J. Chem. Phys. 84(7), 3963 best regard Norge ========================================================================== From: "Jeremy P. Dombroski" Dear Fernando: This is work that myself, Professor Peter Gill and Dr Ross Adamson have spent considerable time on (in particular, the latter). We have recently published an article in J. Comp. Chem. and if you contact Ross at ross@theor.ch.cam.ac.uk he may provide you with a preprint should the article not yet be in print. Q-Chem 1.2 performs O(N) damped Coulomb SCF calculations, including energies, optimizations and frequencies using what we have called the CASE approximation where we replace all occurrences of the Coulomb operator with the so-called Damped Coulomb potential. May I ask where your research interest lies in this damped Coulomb potential? Regards, Jeremy Dombroski ========================================================================== From: "Jan H. Jensen" Hello, I believe Peter Gill at Cambridge has worked on something quite similar. I don't have any references on hand. Best regards, Jan Jensen ******************************************************************************* Fernando D. Vila Department of Chemistry Voice (412)624-8691 University of Pittsburgh Fax (412)624-8552 Box 90 Chevron Science Center E-mail fer@theory6.chem.pitt.edu Pittsburgh, PA 15260, USA WWW http://www.pitt.edu/~fer *******************************************************************************