From chemistry-request@ccl.net Wed Sep 11 21:06:44 1991 Date: Wed, 11 Sep 91 20:49:39 EDT From: Michael A. Lee To: chemistry@ccl.net Subject: Parallel list meets chemistry list Status: R Hello Chemistry mailing list. Probably 90% of the recipients of this are outside of Ohio, so you may not want to spend the time reading. (Skip to PS: at end). For the Ohioans in the crowd, I have a request for an expression of interest in large scale parallel computing in quantum chemistry. Since quantum chemistry probably occupies 30% of the Ohio Supercomputer Center YMP, then I can conclude that there is a big interest in high performance calculations in this area in Ohio. The OSC will be submitting to DARPA in less than 10 days a proposal for a large parallel machine which is MIMD and 2-3 Gigaflops max speed and in the $2M range. We (me and a dozen others) are writing 3-6 pages on science that can be done on such a machine. At the meeting we held yesterday, the invitees from the chemistry community could not attend. If there is a group of Ohioans out there who would like to write about the benefits of large scale parallel quantum chemistry and describe what can be expected in 1-3 years with research support, please let me know. We have a format that I will forward for the 3-6 page chemistry section. As I am grossly overbooked, so I can not organize the writing myself and will want to appoint a head of a chemistry writing team. The description must reflect the diversity of research activities in the State and pay attention to those which DARPA might like especially. Also, most of the communication about this machine has occurred over a different mailing list. There will, for instance, be a provision for individual investigator grants in the proposal. If you are interested in the proposal and/or parallel computing, you may wish to subscribe to the parallel mailing list. The group which makes up the mailing list has been named the Ohio Parallel Computing Consortium. To be on the list and in the consortium are on in the same. You will (after the proposal is finished) learn about plans for workshops etc. in the future. There is a reflector set up for discussion. Mike Lee Send mail to lee@nematic.kent.edu to be added to the list. Send 1. Name, 2. paper address, 3. e-mail address, 4. Phone (regular and FAX) 5. two-sentence research/interest statement. The parallel discussion list is available to non-Ohians, but since I am working on the proposal right now, I can not add a lot of new names until after Sept. 20. Send requests though and they will be added later. My regrets about that. From chemistry-request@ccl.net Thu Sep 12 18:08:46 1991 Date: Thu, 12 Sep 91 17:03:45 EDT From: Joan Groleau To: chemistry@ccl.net Subject: Superimposition Software Status: R The tool that was added to the NIH Prophet System for optimally superimposing two molecular structures in 1984 is based on an algorithm given in the following paper: "Gene Duplications in the Structural Evolution of Chymotrypsin" by A. D. McLachlan, J. Mol. Biol. (1979) 128, 49-79 A Prophet user at Burroughs Wellcome implemented the algorithm for Prophet. The Prophet System is Unix workstation software for biochemical and life science computing that is available for a nominal fee. Feel free to send email to prophet-info@bbn.com if you would like additional information. Joan Groleau for prophet-info@bbn.com