From chemistry-request@ccl.net Mon Mar 9 00:11:33 1992 Date: Sun, 8 Mar 1992 23:13 EST From: "DOUGLAS A. SMITH" Subject: burning time on supercomputers To: chemistry@ccl.net Status: R In response to Jan Labanowski's question, we have one area which still seems to defy current resources, or at least pushes them to the extreme. We have been studying hydrogen bonding in a series of di- and triamides which involve from 8 to 20+ heavy atoms, using molecular mechanics to probe the potential energy surface (you guessed it- the multiple minimum problem). We are now at the stage of beginning to take our tens of minima for each compound, found using the AMBER force field in MacroModel, and submitting each for ab initio single point and geometry optimization. Hydrogen bonding requires massive basis sets for molecules of this size - a recent paper by Pople suggested that RHF/6-31+G** was a minimum requirement, although they did their optimizations at RHF/6-31G* single points at MP2/6-31+G**. We want to also do RPAC calculations of NMR spectra and chemical shift tensors, so the wavefunction must be a good one. These last few requirements are not trivial in and of themselves, but when coupled with 8-10 compounds with from 5-40 minima each, the need for resources just explodes. Regardless, we are trying. Doug Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email fax0236@uoft02.utoledo.edu From chemistry-request@ccl.net Mon Mar 9 11:26:19 1992 Date: Mon, 9 Mar 1992 09:23 EST From: "DOUGLAS A. SMITH" Subject: basis sets for hydrogen bonding To: chemistry@ccl.net Status: R I have already received several requests for the Pople reference I mentioned in my posting about burning supercomputer time. Here it is: Head-Gordon, T.; Head-Gordon, M.; Frisch, M. J.; Brooks, C. L. III, Pople, J. A. J. Am. Chem. Soc. 1991, 113, 5989-97. The paper is titled "Theoretical Study of Blocked Glycine and Alanine Peptide Analogues." I also thought I would pass along this note from Janet Del Bene, who has done a tremendous amount of work on hydrogen bonding, particularly in small molecules such as, but not limited to, HF. Note that if you take Janet's suggestion, my problem gets _much_ larger. Doug Smith +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >Doug, > I was interested to see your comment on the hydrogen-bonding >model. You might be interested in a paper that I am giving at >Sanibel which suggests that geometry optimization at MP2/6-31+G(d,p) >is required, followed by single-point MP4/cc-pVTZ+ single-point >energies. (In some cases, MP2 is okay for the energetics as well, >but a very large basis is needed.) Regards, Janet From chemistry-request@ccl.net Mon Mar 9 11:29:30 1992 Date: Mon, 9 Mar 1992 10:09:50 -0500 From: jkl@ccl.net Subject: Re: Identification of referees To: chemistry@ccl.net Status: R Forwarding to the list ---------- Begin Forwarded Message ---------- Date: Mon, 9 Mar 1992 9:44:02 -0500 (EST) From: EDELSON@EVAX12.ENG.FSU.EDU (Dave Edelson) Subject: Re: Identification of referees To: chemistry-request@ccl.net Most scientific journals maintain the identification of referees as confidential information, they are not known even to the authors unless the referee gives permission. To change this would involve a major rethinking of the entire review process, and I suspect it would become much more difficult for journals to obtain objective reviews for their contributions. David Edelson, Editor Computers and Chemistry ----------- End Forwarded Message ----------- From NU145752@VM1.NoDak.EDU Mon Mar 9 15:41:59 1992 Date: Mon, 09 Mar 92 14:41:18 CST From: Jan Jensen Organization: North Dakota Higher Education Computer Network Subject: Postscript on the Mac To: chemistr@ccl.net Status: R Fellow Netters, This is a question for all you Mac users. Is there a Mac program out there that will take a post script file and render a picture on the screen that one can cut and paste? Our graphics codes produce post script files for hard copies but it would be nice to edit the pictures on the Mac before printing. Any held will be greatly appreciated. Jan H. Jensen Dept. of Chemistry North Dakota State University Fargo, ND 58105 ======================================================================== 5 LINE 1 %DATE LINE 4 %SUBJ LINE 5 %END %IDEND %IDSTART LINE 6 %DIV LINE 25 V900101 %RESUME A question for Mac Users chemistry ccl.net 0 11 8 61 1 0 0 1 1 0 1 0 0 0 25 From chemistry-request@ccl.net Mon Mar 9 18:08:57 1992 Date: Wed, 5 Feb 92 00:56:57 -0500 From: wampler@bchiris.biochem.uga.EDU (John Wampler) Subject: CM-5 To: chemistry@ccl.net Status: R Does anyone have information about the suitability of the Thinking Machines CM-5 for running computational chemistry programs. We are interested in both quantum chemistry and molecular mechanics based calculations (not Monte Carlo). Does anyone have benchmarks that would indicate the % peak performance that might be expected for such codes. Please reply direct to wampler@bchiris.biochem.uga.edu Thanks in advance.. JW From chemistry-request@ccl.net Mon Mar 9 20:12:58 1992 Date: Mon, 9 Mar 92 18:22:54 -0500 From: jle@world.std.COM (Joe M Leonard) Subject: Request for comment To: chemistry@ccl.net Status: R Another along the lines of computationally-intensive cal'n... Since we're in the middle of an explosive growth in computational power (particularly with the advent of mpp machines), I'm curious as to whether it's time to rethink non-bonded cutoffs in MD cal'n. Isn't the physics better if infinite cutoffs are used, and doesn't the force fields get a little easier to parameterize? I'd appreciate folks' thoughts on the matter - directly or via the net. I seem to recall hearing talks on these ideas over the last few years - but I've been wrong before. Restated, are cutoff's VAX-like code remnants (like indirect lists replacing sparse matrices) that should be replaced when one gets the chance? Joe Leonard jle@world.std.com From chemistry-request@ccl.net Mon Mar 9 20:16:45 1992 Date: Mon, 9 Mar 92 19:02:51 EST From: "Michael A. Lee" Subject: An opinion on referee identification To: chemistry@ccl.net Status: R Having just read the e-mail of David Edelson, Editor Computers and Chemistry, I am a little surprized that there has been so few comments on this subject. Presumably this is not a question of anonymity. I assume a rejected paper would not result in the name of the referee being given to the authors. I suspect this is an issue on Quality. Would you as a referee be willing to put your name on a piece of junk? Would you as a referee make the kind of inane comments which are made by some referees if you knew that your identity would become public? Actually, it sounds like a good idea to me. I predict that I would have fewer and higher quality articles filling the volumes in my library. Mike Lee Physics, Kent State