From ronnie@batata.fh.huji.ac.il Wed Dec 8 04:54:01 1993 Received: from batata.fh.huji.ac.il for ronnie@batata.fh.huji.ac.il by www.ccl.net (8.6.4/930601.1506) id EAA09542; Wed, 8 Dec 1993 04:13:33 -0500 Received: by batata.fh.huji.ac.il (920330.SGI/911001.SGI/930210.fh.huji.ac.il) for CHEMISTRY@ccl.net id AA25857; Wed, 8 Dec 93 11:14:03 +0200 Date: Wed, 8 Dec 93 11:14:03 +0200 From: ronnie@batata.fh.huji.ac.il (Ronnie Kosloff) Message-Id: <9312080914.AA25857@batata.fh.huji.ac.il> To: CHEMISTRY@ccl.net Subject: Embedded atom method Dear netters, May be anybody knows about Embedded atom method (EAM) program which is available in Pablic Domain. I want to use this program to calculate interactions of hydrogen with various transition metal surfaces. If anybody knows of such a programs please inform me about its telnet or ftp location. Thanks Ronnie Kosloff From ferenc@rchsg8.chemie.uni-regensburg.de Wed Dec 8 06:54:03 1993 Received: from rrzs1.rz.uni-regensburg.de for ferenc@rchsg8.chemie.uni-regensburg.de by www.ccl.net (8.6.4/930601.1506) id GAA10099; Wed, 8 Dec 1993 06:16:11 -0500 Received: from rchsg8.chemie.uni-regensburg.de by rrzs1.rz.uni-regensburg.de (4.1/URRZ-relay (1.4)) id AA19513; Wed, 8 Dec 93 12:15:26 +0100 Received: by rchsg8.chemie.uni-regensburg.de (920330.SGI/BelWue-1.0SG(subsidiary)) (for CHEMISTRY@ccl.net) id AA28566; Wed, 8 Dec 93 12:16:18 +0100 Date: Wed, 8 Dec 93 12:16:18 +0100 From: ferenc@rchsg8.chemie.uni-regensburg.de (Ferenc Molnar) Message-Id: <9312081116.AA28566@rchsg8.chemie.uni-regensburg.de> To: CHEMISTRY@ccl.net Subject: constraints Dear Netters! There are two questions I would like to discuss with you. The first one deals with constraints in molecules. How can I claculate the constrained virial if I use RATTLE as an algorithm to solve the constrained problem? Do I have to take the constrained virial into account when I calculate the pressure of the system ? I think so, but I am not sure how to do it. The second problem is a different one. Somewhere I read about the following phenomenon. In the simulation of solvens-solute interactions the solute tends to cool and the solvent warms up. Can anybody give me a hint on where to find information on this topic. Thanks in advance. Ferenc Ferenc Molnar --------------------------------------------------------------------------- Institut fuer Physikalische und Theoretische Chemie - Lehrstuhl Prof. Dick - Tel.: (+49) 941 943-4466 /-4486 Universitaet Regensburg Fax.: (+49) 941 943-4488 Universitaetsstrasse 31 D-93053 Regensburg Deutschland / Germany --------------------------------------------------------------------------- EMail (SMTP): ferenc@rchsg8.chemie.uni-regensburg.de c5071@rchs1.chemie.uni-regensburg.de ferenc@rchnw2.ngate.uni-regensburg.de --------------------------------------------------------------------------- :-) There is more to live than increasing its speed. -- Ghandi ;-) --------------------------------------------------------------------------- From dodik@yfaat.ch.huji.ac.il Wed Dec 8 09:54:13 1993 Received: from shum.cc.huji.ac.il for dodik@yfaat.ch.huji.ac.il by www.ccl.net (8.6.4/930601.1506) id IAA11002; Wed, 8 Dec 1993 08:55:55 -0500 Received: from yfaat.ch.huji.ac.il by shum.cc.huji.ac.il with SMTP id AA00337 (5.65cHU/IDA-1.4.4 for ); Wed, 8 Dec 1993 15:55:42 +0200 Received: by yfaat.ch.huji.ac.il (AIX 3.2/UCB 5.64/4.03) id AA23658; Wed, 8 Dec 1993 11:10:27 +0200 Date: Wed, 8 Dec 1993 11:10:27 +0200 From: dodik@yfaat.ch.huji.ac.il (David Danovich) Message-Id: <9312080910.AA23658@yfaat.ch.huji.ac.il> To: CHEMISTRY@ccl.net Subject: Embedded atom method Dear netters, May be anybody knows about Embedded atom method (EAM) program which is available in Pablic Domain. I want to use this program to calculate interactions of hydrogen with various transition metal surfaces. If anybody knows of such a programs please inform me about its telnet or ftp location. Thanks David Danovich From fant@fconvx.ncifcrf.gov Wed Dec 8 10:54:17 1993 Received: from fconvx.ncifcrf.gov for fant@fconvx.ncifcrf.gov by www.ccl.net (8.6.4/930601.1506) id KAA11964; Wed, 8 Dec 1993 10:28:57 -0500 Received: by fconvx.ncifcrf.gov (5.64/10.1) id AA01081; Wed, 8 Dec 93 10:28:53 -0500 Date: Wed, 8 Dec 93 10:28:53 -0500 From: fant@fconvx.ncifcrf.gov (Andrew D. Fant) Message-Id: <9312081528.AA01081@fconvx.ncifcrf.gov> To: chemistry@ccl.net Subject: Compatability of Ab Initio results from different software Packages Does anyone have any experience in how well Hartree-Fock energies calculated by Gaussian 92 correlate with the same species calculated under GAMESS? The results are consistent with the trends I had been seeing under one program, and they are also in agreement with the AM1 results I got from MOPAC. I know that given the same basis set and geometry the results OUGHT to be identical, but I am becoming more paranoid about numerical methods in general lately, and I wanted to see if anyone had made a well-considered examination of this question. For what it's worth: I did make a very small comparison (about 6 data-points) between G92 and Spartan, and for HF and MP2, the energies of molecules geometry optimized by the respective programs were identical to the precision of the platforms used. Thanks for your input. Andy Andrew D. Fant Applications Analyst fant@ncifcrf.gov NCI-Frederick Cancer Research Facility Biomedical Supercomuting Center (301)846-5764 Me?!? Have an official NCI or Dyncorp Opinion? HAH! "I'm just one too many mornings and a thousand miles behind" -- B. Dylan From berkley@wubs.wustl.edu Wed Dec 8 10:56:47 1993 Received: from wugate.wustl.edu for berkley@wubs.wustl.edu by www.ccl.net (8.6.4/930601.1506) id KAA12000; Wed, 8 Dec 1993 10:32:17 -0500 Received: by wugate.wustl.edu (5.67a+/WUSTL-0.3) with SMTP id AA16643; Wed, 8 Dec 1993 09:32:05 -0600 Received: by wubs.wustl.edu; (5.65/1.1.8.2/14Oct93-1217PM) id AA15146; Wed, 8 Dec 1993 09:34:46 -0600 Date: Wed, 8 Dec 1993 09:34:46 -0600 From: "Mr. Berkley Shands" Message-Id: <9312081534.AA15146@wubs.wustl.edu> To: chemistry@ccl.net Subject: Benchmarks of new systems Once again I can provide benchmarks of new systems, with FULL compiler optimizations in place. Actual configurations used are reported. I would suggest a minimum of 64 MB on any DEC AXP system. If you want SYBYL on the DEC AXP series, better ask Tripos. Most other packages run on the Alpha already. Berkley Receptor-III (TM - Tripos Associates) Beta Release version V2.4 timings for the ACE series. Uniform distance space scanning at 0.05A maximum increment with Adaptive Scanning in modified mode applied. All bonds Adaptively scanned. Minimum scan factor 0.45 degrees, maximum scan factor 2.81 degrees. ******************************************************************************* Benchmarks of the complete ACE series of 71 molecules Modified scan factors ******************************************************************************* Elapsed Child_CPU System_CPU Chargable Forks Ratio ======= ========= ========== ========= ===== ===== 979 912.880 37.650 887.840 7 0.937 SGI Indigo 48Mb -O2 (R3K/33Mhz) 926 855.010 55.830 829.661 7 0.929 SGI 4d/380s 128Mb -O2 (R3K/33Mhz) 740 587.350 9.200 557.883 7 0.805 DEC 3K/300L AXP 32Mb STD "CC" -O2 726 562.350 11.650 533.950 7 0.785 DEC 3K/300L AXP 32Mb GEM "CC" -O4 661 558.133 5.083 541.450 7 0.852 E&S ESV M120 -O2 (R3K/45Mhz) 783 472.460 8.340 461.310 7 0.606 SGI Indigo2 64Mb -O2 -mips2 (R4K/50Mhz) 594 455.130 5.680 443.570 7 0.774 SGI Challenge M 96Mb -O2 (R4K/100Mhz) 481 453.650 3.917 430.500 7 0.953 DEC 3K/300 AXP 32mb STD "CC" -O2 411 381.400 4.100 363.817 7 0.939 DEC 3K/300 AXP 32mb GEM "CC" -O4 527 364.010 4.910 352.730 7 0.700 SGI Challenge M 96Mb -O3 -mips2 (R4K/100Mhz) 359 325.133 4.150 308.433 7 0.916 DEC 3K/300 AXP 32mb GEM "CC" -O4 -feedback 239 212.367 1.503 200.117 7 0.904 DEC 3K/600 AXP 128mb GEM "CC" -O4 -feedback 201 187.817 1.333 177.183 7 0.949 DEC 3K/800 AXP 256mb GEM "CC" -O4 -feedback ******************************************************************************* Notes: DEC AXP 3000/300L is 100 Mhz, 3K/300 is 150 Mhz, 3K/600 is 175 Mhz, 3K/800 is 200 Mhz Many thanks to DEC for providing the 3K/600 and 3K/800 Machines. The "GEM" compiler is in save set CMPDEVENH on the OSF/1 CD. The "STD" compiler is the default "CC" for OSF/1. KAP-C was not used; generated code hits a compiler bug in one routine :-( "Child_CPU" is the recorded total CPU for all forked processes, including overhead and I/O. "Elapsed" is the recorded elapsed time from command line parsing to the exit of the last child processes. "System_CPU" is the recorded UNIX system overhead from the times() function "Chargable" is the algorithmic chargable time from initial rotations to termination (child process CPU) ***************************************************************************** From jmcohen@cbdcom.apgea.army.mil Wed Dec 8 13:54:47 1993 Received: from cbdcom.apgea.army.mil for jmcohen@cbdcom.apgea.army.mil by www.ccl.net (8.6.4/930601.1506) id NAA14525; Wed, 8 Dec 1993 13:43:04 -0500 Received: by cbdcom.apgea.army.mil id aa15888; 8 Dec 93 13:37 EST Date: Wed, 8 Dec 93 13:30:03 EST From: "Joel M. Cohen" To: chemistry@ccl.net Subject: how to books Message-ID: <9312081330.aa13542@cbdcom.apgea.army.mil> Dear netters, I wish to add a few how to books of general interest to my library. Specifically: how to optimize code (general) how to optimize FORTRAN code how to optimize C code how to write code for parallel computers Any suggestions? Dr. Joel Cohen From szilagyi@miat0.vein.hu Wed Dec 8 13:57:39 1993 Received: from sztaki.hu for szilagyi@miat0.vein.hu by www.ccl.net (8.6.4/930601.1506) id NAA14606; Wed, 8 Dec 1993 13:50:35 -0500 Received: by sztaki.hu with SMTP (5.67a8/SZTAKI-3.13) id OG02443; Wed, 8 Dec 1993 19:49:46 +0100 Received: by miat0.vein.hu (5.61++/Vein-1.0) id AA15106; Wed, 8 Dec 93 19:51:21 +0100 Date: Wed, 8 Dec 93 19:51:21 +0100 From: Szilagyi Robert Message-Id: <9312081851.AA15106@miat0.vein.hu> To: chemistry@ccl.net, fant@fconvx.ncifcrf.gov Subject: Re: Compatability of Ab Initio results from different software Packages X-Charset: US X-Char-Esc: 0 Dear Andy, I tested the g92 and the GAMESS packages on tungsten carbene complexes, using ECPs. The GAMESS with SBK ECP is much better than the G92 LANL1MB or LANL1DZ. Now I am going to test the origin of the differences. They are due to the basis set or the software. I will summarize the results on net and to you of course. Cheers, Rob From cletner@remcure.bmb.wright.edu Wed Dec 8 13:58:24 1993 Received: from remcure.bmb.wright.edu for cletner@remcure.bmb.wright.edu by www.ccl.net (8.6.4/930601.1506) id NAA14358; Wed, 8 Dec 1993 13:33:41 -0500 Received: by remcure.bmb.wright.edu (920330.SGI/921111.SGI.AUTO) for CHEMISTRY@ccl.net id AA16470; Wed, 8 Dec 93 13:32:10 -0800 Date: Wed, 8 Dec 1993 13:06:32 -0800 (PST) From: Charles Letner Subject: Protein Force fields To: Computational Chemistry List Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all, Last week I posted a question concerning the kollman all-atom vs the kollman united-atom force field. I later sent a couple of references to the board. One of these by Kini and Evans. I just found another paper by them from 1992 that I thought some of you might be interested in. It compares the all-atom and united-atom versions of the kollman force field. That reference is: Kini, R. M., and Eveans, J. E., Comparison of Protein Models Minimized by the All-Atom and United-Atom Models in the AMBER Force Field: Correlation of RMS deviation with Crystallographic R Factor and Size, J. Biomol. Str. & Dyn., 10, 2 (1992) pg. 265-279. Having said that, I've also just finished the series of two papers by Roterman, Lambert, Gibson, and Scheraga (1989) from J. Biomol. Stru. & Dyn. These papers have me kind of stumped. These papers compare CHARMM, AMBER, and ECEPP for modeling proteins. If I read them right they come down pretty hard on these force fields. In fact the last line of the second paper says that conformational studies by these force fields may give results that are "entirely misleading". Further, they state that the AMBER force field may be inappropriate for dynamics simulations. I'm getting ready to start some dynamics simulations using AMBER. Obviously I'm somewhat concerned now. I would sincerely appreciate any comments some of you might have on this paper. Also any comments or references that would help understand the validity of M/M and dynamics would be welcome. Thanks and I am looking forward to your comments. Chuck Charles Letner Wright State University Department of Biochemistry Dayton, OH 45435 e-mail: cletner@remcure.bmb.wright.edu From mizan@rz.engin.umich.edu Wed Dec 8 14:54:08 1993 Received: from rz.engin.umich.edu for mizan@rz.engin.umich.edu by www.ccl.net (8.6.4/930601.1506) id OAA15562; Wed, 8 Dec 1993 14:46:01 -0500 Received: by rz.engin.umich.edu (5.67/1.35) id AA09002; Wed, 8 Dec 93 19:45:59 GMT Date: Wed, 8 Dec 93 19:45:59 GMT From: "Tahmid I. Mizan" Message-Id: <9312081945.AA09002@rz.engin.umich.edu> To: CHEMISTRY@ccl.net Subject: van der Waals parameters Hi, I address my question (probably a trivial question) to any obliging molecular dynamics guru: Weiner, et al. (J. Comp. Chem. 7,230-252,1986) report non-bonded parameters for an aliphatic all atom carbon (sp3) as R* = 1.80 angstrom and epsilon = 0.06 kcal/mol. I assume this corresponds to a sigma, sigma = R*/2^(1/6) so that for the carbon sigma = 1.604 angstrom but most other sources give much larger values of sigma, sigma = 3.35 angstrom (Allen & Tildesley, p.21) What am I missing here ? Obviously one value is about double the other, why ? Thanks in anticipation. Tahmid Mizan mizan@engin.umich.edu ) What am I missing here ? Obviously one value is about double the other, why ? Thanks in anticipation. Tahmid Mizan mizan@engin.umich.edu From case@scripps.edu Wed Dec 8 15:56:43 1993 Received: from scripps.edu for case@scripps.edu by www.ccl.net (8.6.4/930601.1506) id PAA15994; Wed, 8 Dec 1993 15:27:04 -0500 Received: from lanczos.scripps.edu by scripps.edu (5.61/1.34) id AA15649; Wed, 8 Dec 93 12:26:55 -0800 Received: by lanczos.Scripps.EDU (4.1/SMI-4.1) id AA12209; Wed, 8 Dec 93 12:26:03 PST Date: Wed, 8 Dec 93 12:26:03 PST From: case@scripps.edu (David Case) Message-Id: <9312082026.AA12209@lanczos.Scripps.EDU> To: chemistry@ccl.net Subject: Re: Protein Force fields Charles Letner wrote: > > Having said that, I've also just finished the series of two papers > by Roterman, Lambert, Gibson, and Scheraga (1989) from J. Biomol. Stru. & > Dyn. These papers have me kind of stumped. These papers compare CHARMM, > AMBER, and ECEPP for modeling proteins. If I read them right they come > down pretty hard on these force fields. In fact the last line of the > second paper says that conformational studies by these force fields may > give results that are "entirely misleading". Further, they state that the > AMBER force field may be inappropriate for dynamics simulations. I'm > getting ready to start some dynamics simulations using AMBER. Obviously > I'm somewhat concerned now. I would sincerely appreciate any comments > some of you might have on this paper. Peter Kollman and Ken Dill wrote a reponse to this paper: "Decisions in Force Field Development: An Alternative to those Described by Roterman et al." J. Biomol. Struct. Dyn. 8:1103-1107 (1991) which is worth looking at. Charlie Brooks and I also considered some of the arguments in the Roterman et al papers in our recent article in Chemical Reviews, 93: 2487-2502 (1993). My view is that the phrase "entirely misleading" is a little harsh, but it clearly depends on what aspects of the calculations you are looking at. Roterman et al do make a good point that some pretty fundamental features of protein conformations are different with different force fields, and one needs to be very careful in interpreting simulation results. There are often features of dynamics simulations that are quite insensitive to the details of the force field; you might want to consider a paper that Martha Teeter and I wrote for some examples: J. Phys. Chem. 94: 8091-8097 (1990). You might also want to consider some of the work of Julian Tirado-Rives and Bill Jorgensen, e.g. JACS 112:2773-2781 (1990) and references therein to earlier work. This list just scratches the surface, but it may help you to get started. Hope this helps....dave case From m10!aefrisch@uunet.UU.NET Wed Dec 8 16:54:13 1993 Received: from relay1.UU.NET for m10!aefrisch@uunet.UU.NET by www.ccl.net (8.6.4/930601.1506) id QAA17140; Wed, 8 Dec 1993 16:19:50 -0500 Received: from spool.uu.net (via LOCALHOST) by relay1.UU.NET with SMTP (5.61/UUNET-internet-primary) id AA26151; Wed, 8 Dec 93 16:19:21 -0500 Message-Id: <9312082119.AA26151@relay1.UU.NET> Received: from m10.UUCP by uucp6.uu.net with UUCP/RMAIL (queueing-rmail) id 161648.7568; Wed, 8 Dec 1993 16:16:48 EST Received: by m10.gaussian.com; Wed, 8 Dec 93 14:54:16 EST Date: Wed, 8 Dec 93 14:54:16 EST From: m10!aefrisch@uunet.UU.NET (AEleen Frisch) Subject: Re: how to books To: "Joel M. Cohen" Cc: chemistry@ccl.net In-Reply-To: "Joel M. Cohen" , Wed, 8 Dec 93 13:30:03 EST Dear netters, I wish to add a few how to books of general interest to my library. Specifically: how to optimize code (general) how to optimize FORTRAN code Consider High Performance Computing by Kevin Dowd from O'Reilly and Associates. ------- From theresa@si.fi.ameslab.gov Wed Dec 8 16:55:06 1993 Received: from si.fi.ameslab.gov for theresa@si.fi.ameslab.gov by www.ccl.net (8.6.4/930601.1506) id QAA16903; Wed, 8 Dec 1993 16:02:09 -0500 Received: by si.fi.ameslab.gov (AIX 3.2/UCB 5.64/4.03) id AA28739; Wed, 8 Dec 1993 15:02:04 -0600 From: theresa@si.fi.ameslab.gov (Theresa Windus) Message-Id: <9312082102.AA28739@si.fi.ameslab.gov> Subject: Re: Compatability of Ab Initio results To: chemistry@ccl.net Date: Wed, 8 Dec 93 15:02:03 CST X-Mailer: ELM [version 2.4beta PL7] Content-Type: text Content-Length: 1784 Dear netters: In reply to: >From: Szilagyi Robert >Dear Andy, > > I tested the g92 and the GAMESS packages on >tungsten carbene complexes, using ECPs. > > The GAMESS with SBK ECP is much better than >the G92 LANL1MB or LANL1DZ. Now I am going to test >the origin of the differences. They are due to the basis >set or the software. I will summarize the results on net >and to you of course. > >Cheers, > > Rob I am sure Rob will find that the major difference is the basis set. We have run many tests and the general conclusion is that GAMESS and GAUSSIAN give the same energy (out to the seventh decimal place) IF the same basis set, number of d's (6 or 5), geometry and wavefunction are used. Occasionally, different energies will result from different initial guesses. These are generally cases where the initial guess creates a wavefunction of the "wrong" symmetry (i.e. not the ground state symmetry). Either program will occasionally come up with the "wrong" initial guess. Since GAMESS and GAUSSIAN use different optimization routines, different geometries CAN be found. Usually, however, for the same initial geometry and same initial hessian the same final geometry is found (within chemical accuracy). I am probably biased, but I have generally found that transition states are easier to find in GAMESS. I have had a couple of occasions where I couldn't find a transition state with GAUSSIAN (given a "not too bad" starting geometry) that GAMESS found in about 10-15 steps. Optimization or transition state searches are "tricky" things and the algorithm used can occasionally do different things. Hope this helps! Theresa Windus Department of Chemistry Iowa State University Ames, IA 50011 e-mail: theresa@si.fi.ameslab.gov From mf10101@s1.msi.umn.edu Wed Dec 8 16:56:43 1993 Received: from s1.msi.umn.edu for mf10101@s1.msi.umn.edu by www.ccl.net (8.6.4/930601.1506) id QAA17203; Wed, 8 Dec 1993 16:24:39 -0500 Received: from s6.msi.umn.edu by s1.msi.umn.edu; Wed, 8 Dec 93 15:24:25 -0600 Date: Wed, 8 Dec 93 15:24:26 CST From: "Jan Amlof [uc migration account]" Message-Id: <9312082124.AA20485@s6.msi.umn.edu> Received: by s6.msi.umn.edu; Wed, 8 Dec 93 15:24:26 CST To: CHEMISTRY@ccl.net Subject: Winter School in Computational Chemistry. Dear colleague, Since 1989, the Theoretical Chemistry Group in Lund, Sweden has organized a biennial European Summer School in Quantum Chemistry, teaching the theory and methods of modern computational quantum chemistry to graduate students and postdocs in theoretical chemistry, as well as to students and researchers at a corresponding level from other areas of chemistry and from industry. The teachers at this summer school have included Jan Almlof, Nicholas Handy, Trygve Helgaker, Per-Ake Malmqvist, Jeppe Olsen, Bjorn Roos, Peter Taylor, and Ulf Wahlgren. The courses have covered Hartree-Fock, MCSCF, CI, coupled-cluster, energy derivatives, relativistic effects, magnetic & time- dependent properties, second quantization, mathematical tools, effective core potentials, and density functional theory. The courses involve both lectures and supervised exercises/tutorials. The school lasts for two weeks and is held at an isolated location in southern Sweden. In the past, $800-900/student has covered food, lodging and all of the course material (the school is run on a non-profit, cost recovery basis.) The two "American" members of the team (JA & PT) are now trying to transplant the idea to the American continent (specifically, southern California). The school would take place during the first two weeks of January 1995, and we are looking towards an attendance of 50-75 students. However, before proceeding further we have decided to canvass the community for an indication of the interest for such an endeavor. At this point of the planning we find it important to distinguish encouraging pats on the back in general from predictions bordering on a tentative commitment. If the idea is not going to fly, we'd like to know that now, rather than find ourselves lecturing to empty seats in 1995! Since we have not explored possibilities for external funding yet, we cannot predict the cost with any certainty, and we therefore request your opinion on several different scenarios, listed below: We ask for your cooperation in returning the bottom part of this inquiry by the end of December. Please forward this message to any other colleague who might be interested in our endeavor. _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ NAME: _______________________________________ ____________ I like the idea, but cannot predict participation >from my institution at this time. ____________ I expect that I would send __ people if the cost turns out to be $700/person or less. ____________ I would probably send __ people at a cost of no more than $1,200/person. Additional comments are appreciated. Please respond before Dec. 31 to: Jan Almlof or: almlof@chemsun.chem.umn.edu Department of Chemistry University of Minnesota Minneapolis, MN 55455 From ross@cgl.ucsf.EDU Wed Dec 8 19:54:11 1993 Received: from socrates.ucsf.EDU for ross@cgl.ucsf.EDU by www.ccl.net (8.6.4/930601.1506) id TAA19071; Wed, 8 Dec 1993 19:13:21 -0500 Received: from localhost by socrates.ucsf.EDU (8.6.4/GSC4.24) id QAA24226; Wed, 8 Dec 1993 16:13:16 -0800 Date: Wed, 8 Dec 1993 16:13:16 -0800 Message-Id: <199312090013.QAA24226@socrates.ucsf.EDU> From: ross@cgl.ucsf.edu (Bill Ross ) To: chemistry@ccl.net Subject: van der Waals parameters From: "Tahmid I. Mizan" I address my question (probably a trivial question) to any obliging molecular dynamics guru: Perhaps I'm not a guru, but here's what I know: Van der Waals interactions are parameterized by Lennard-Jones (L-J) '6-12' potentials of the form E = AiAj/r^6 - BiBj/r^12 where A and B parameters for the types of atoms i and j are derived for the potential between two atoms of the same type. This same-type potential curve can also be defined by the radius (r *) corresponding to half the internuclear distance at the point of minimum energy, and the potential well depth ('e') at that internuclear distance. In this convention the potential energy for the van der Waals interaction between atoms 'i' and 'j' is defined as (r*ij, eij), where r*ij is (r*i + r*j), and eij is sqrt(eiej). This is the convention which is used by AMBER. So sigma is the internuclear distance at the potential minimum for two atoms, corresponding to R*ij. R* for a single atom corresponds to the sound of one hand clapping, in that it can mislead one to think that if the universe consisted of a single atom, that atom would have a size. Bill Ross From pkarp@ai.sri.com Wed Dec 8 20:54:12 1993 Received: from Sunset.AI.SRI.COM for pkarp@ai.sri.com by www.ccl.net (8.6.4/930601.1506) id UAA19539; Wed, 8 Dec 1993 20:51:26 -0500 Received: from Bolinas.AI.SRI.COM by Sunset.AI.SRI.COM (4.1/SMI-4.1) id AA02805 for chemistry@ccl.net; Wed, 8 Dec 93 17:50:49 PST Received: by Bolinas.AI.SRI.COM (4.1/SMI-4.1) id AA28126 for chemistry@ccl.net; Wed, 8 Dec 93 17:50:47 PST Date: Wed, 8 Dec 93 17:50:46 PST From: Peter Karp To: chemistry@ccl.net Subject: Seeking DB of biochemical compounds Message-Id: I am working on a project that involves constructing a database of E. coli biochemistry. I am seeking a database of biochemical compounds (amino acids, carbohydrates, etc -- compounds that act as enzyme substrates). Preferably the database would be public domain and/or inexpensive. Associated retrieval software for the database is not important to me -- I wish to import it into the software environment we are developing. The data I am most interested in having is compound structures and many synonyms per compound name. If anyone can give me pointers to such a database, I would appreciate it. Please respond to me directly as I do not read this list. Peter Karp pkarp@ai.sri.com From anthony.scott@anu.edu.au Wed Dec 8 23:54:14 1993 Received: from anu.anu.edu.au for anthony.scott@anu.edu.au by www.ccl.net (8.6.4/930601.1506) id XAA19988; Wed, 8 Dec 1993 23:14:34 -0500 Received: from cscgpo.anu.edu.au by anu.anu.edu.au (4.1/SMI-4.1) id AA11070; Thu, 9 Dec 93 15:12:32 EST Received: from huxley.anu.edu.au by cscgpo.anu.edu.au (4.1/SMI-4.1) id AA21142; Thu, 9 Dec 93 15:14:57 EST Date: Thu, 9 Dec 93 15:14:57 EST From: anthony.scott@anu.edu.au (Anthony P Scott) Message-Id: <9312090414.AA21142@cscgpo.anu.edu.au> To: CHEMISTRY@ccl.net Subject: QCPE 611 (Vibrate) We have the vibrate program from qcpe (611) mounted on a SGI and it works fine. However we have an IBM/RS6000 355 and would also like to get it running on that machine also. Has anyone done this. We have tried to compile it and it seems as though it requires a header file (fget.h) that exists on the SGI but not on the IBM. Any ideas anyone. Oh by the way this program takes Gaussian log file output for a frequency job and displays the an animation of the normal modes. Thanks in advance. Tony Scott Research School of Chemistry Australian National University Canberra, ACT, Australia