From m10!frisch@uunet.UU.NET Thu May 6 21:17:00 1993 Message-Id: <9305070515.AA08946@relay2.UU.NET> Date: Fri, 7 May 93 01:17:00 EDT From: m10!frisch@uunet.UU.NET (Michael Frisch) Subject: Gaussian 92 and NFS mounted files To: chemistry@ccl.net While we recommend that you avoid using remote file systems for Gaussian scratch files, we also intend that they function properly. It is not possible for us to test every combination of type of compute machine and type of file server, the combinations we can test do work. The error which was reported (running on Convex with files on an Indigo) looked like there was some problem with the file size information provided to Gaussian. Since I can run here on either a Sun or an RS/6000 with scratch fiies on an SGI, I presume that the problem is on the Convex side. Mike Frisch ------- From chp1aa@surrey.ac.uk Fri May 7 06:16:35 1993 From: Mr Andrew D Allen Message-Id: <9305070900.AA08072@central.surrey.ac.uk> Subject: Conflicting energies from MM2 and MM+ To: CHEMISTRY@ccl.net Date: Fri, 7 May 93 10:00:04 BST Dear Fellow modellers, I have recently been using the MM2 force field on MSI's Biograf (Ver 2.20) getting minimised energies in the 100 - 120 Kcal ballpark. Our department here in Surrey, recently obtained Hyperchem, so to back up the work I have done I run a similiar conjugate energy minimisation on some of my molecules taken from Biograf in a Brookhaven format. The resulting energies after minimisation were around 40 - 50 Kcals. In some cases nearly a third of the energy obtained from Biograf. Intrigued? I was. Checking further I had a colleague run a similiar calculation on the same molecules using the CHRAMM force field and the energies came out around 40 - 50 Kcals. Question: Is the MM2 force field in Biograf wrong? Question: Has anyone else experienced widely different energies using different force - fields. ANDY. From chris@desor.tc.cornell.edu Fri May 7 05:39:59 1993 Date: Fri, 7 May 1993 09:39:59 -0400 From: chris@desor.tc.cornell.edu (Chipot Christophe) Message-Id: <9305071339.AA42315@desor.tc.cornell.edu> To: chemistry@ccl.net Subject: ESP_Charges Dear Netters, Here are a few remarks concerning Joe Leonard's and Rob Woods's comments on ESP-charges: We have studied the problematic of point charge models derived from ab initio electrostatic properties (potential, field and distributed multipole moments), and this is our point of view: Rob Woods: 'we found that HF/6-31G* ESP-charges could lead to an excellent reproduction of the SCF-dipole moment...' Well, this is not really surprising, especially for polar species, where the dipole is the predominant term of the multipolar expan- sion. In addition, the long-range effect of the dipole moment is adapted to most grid definitions, so that this component is easily reproduced in the fitting procedure. This is not completely the case for the multipole moments of higher orders, and I doubt you will get 'an excellent reproduction' of hexadecapoles, particularly if you deal with nonpolar species (Chipot et al., J. Phys. Chem., in press) Rob Woods: 'We and others (Breneman and Wiberg, J. Comput. Chem. 11 (1990) 361) have noted that charge convergence requires that the ESP should be sampled at a surprisingly high density of points' Here is the typical problem of grid definition. As it has been pointed out by Colonna et al., and confirmed by our experience, the variations of the charges, supposedly due to some grid modifications, is, in fact the result of penetration. If, indeed, you fit the charges to the ESP that has been contaminated by pene- tration, i.e. under-evaluation of the vdW envelope, your results will be quite suspicious. Increasing the sampling density will merely conceal the fitting errors due to the contamination. There are two alternatives to remedy this deficiency: - use a potential created by overlap multipole moments (Colonna et al., J. Comp. Chem., 1992, 13, 1234), or distributed multipole moments (Ferenczy, J. Comp. Chem., 1991, 12, 913; Chipot et al., J. Phys. Chem., in press), hence neglecting the effects of penetration and dealing with the exact multipolar part of the ESP exclusively. - over-dimension the vdW envelope (Chipot et al., J. Phys. Chem., 1992, 96, 10276), so that penetration is avoided, but multipole moments of higher order than dipoles will nonetheless be taken into account. Incidentally, the 'excellent reproduction of the SCF-dipole moment' will be true, as far as your molecule does not bear any lone pairs. In the latter case, you should include some atomic dipoles, and even quadrupoles, in addition to the point charges, or, at least, use a set of off-atom point charges to mimic the effects of the above moments. Hope this will help....... Chris Chipot, Laboratoire de Chimie Theorique Universite de Nancy I BP. 239 54506 Vandoeuvre-les-Nancy (France) From wiedeman@altair.acs.uci.edu Fri May 7 00:53:26 1993 To: chemistry@ccl.net Subject: G92 and NFS Date: Fri, 07 May 93 07:53:26 -0700 Message-Id: <599.736786406@altair.acs.uci.edu> From: Lyle Wiedeman Gee, I certainly got all the discussion I could have wanted, and more! I've seen a range of opinions: * G92 wasn't meant to work through NFS * You'd be an idiot to use NFS; it's cheaper to go DIRECT * Some of us have no choice but to use NFS * G90 had bugs, but G92 is fixed * Convex G92 must be at fault, because the Sun works with the Indigo #3 is where we stand: we have G92 only one place on campus, a central time-sharing machine which is reasonably fast, had LOTS of core memory, and (for most applications) a large amount of disk space. Unfortunatly, with G92 creating files of 1GB and up, "lots" of disk space is never enough on a shared machine. Worse, researchers here generally cannot afford to pay for 1GB of ongoing disk space on the central machine; it is MUCH more economical for them to get 1, 2, or more GB of cheap SCSI disk on their individual workstations, and access it through NFS. I am still curious about the performance tradeoffs (DIRECT vs. NFS), so any reports will be appreciated. Also, I am sure I will hear from the Convex G92 porting team soon. Thanks, one and all, even those who called us stupid and insane :-) Lyle Wiedeman Office of Academic Computing wiedeman@uci.edu Univ. Calif. Irvine wiedeman@UCI.BITNET Irvine, CA 92717 (714) 856-8718 FAX (714) 725-2069 From dmschn@bb1t.monsanto.com Fri May 7 05:10:23 1993 Date: Fri, 7 May 93 10:10:23 -0500 Message-Id: <9305071510.AA09275@tin.monsanto.com> From: dmschn@bb1t.monsanto.com To: "chemistry@ccl.net"@tin.monsanto.com Subject: conflicting energies from MM2 and mm+ There is no reason to expect that different force fields will yield the same ene regies. The result is dependent on the potentials used in the force field and th e parameter set for the functional groups. There are many versions of MM2 out and about since the parameter sets have grown ever the years. Many people have implemented force fields based on MM2 but that have slightly (or not so slightly )differing potential equations. Allinger's group has released several versions over the years: 82,85,87,91 to mention a few. Most of these produce fairly consi stent results--energy differences should be small. Commercial implementations tend to get around the the parameter problem(the ones you need usually just aren 't there) by putting in some kind of standard estimates(frequently poor) just so that the program will run for the non molecular mechanics specialist. I have not looked at MSI's MM2 implementation or that in Hyperchem but I suspect that parameter estimates are the reason for the large energy differences. This is assuming that they are actually using Allinger's force field in one of it's early incarnations. As to whether on of the force fields is actually "wrong", I would reccommend actually running Allinger's MM2, preferable MMP2(91). He has often received complaints about MM2 that turned out to in fact be complaints about someone else's personal implementation based on his publications. It has been a source of distress over the years. Dora Schnur dmschn@bb1t.monsanto.com From dave@terminus.chem.yale.edu Fri May 7 07:48:40 1993 From: David Maxwell Message-Id: <9305071548.AA12884@terminus.chem.yale.edu> Subject: Re: Conflicting energies for different force fields To: CHEMISTRY@ccl.net Date: Fri, 7 May 93 11:48:40 EDT Hello, I am replying to the question about widely different energies from different force fields. It is normal for different force fields to differ for the same calculation on the same molecule, because the component energies in different force fields are not always calculated in the same manner. In addition, a component like the non-bonded term may have different parameters, although the form is the same. Example ------- A calculation with Macromodel for cyclohexane in chair form Force field E (kcal/mol) --------------------------- MM2 6.55 MM3 8.04 AMBER 1.72 OPLS 0.91 These are values after optimizing with the default settings. Does this mean that the force fields are wrong in Macromodel? Absolutely not! It is only useful to compare the relative energies between force fields. Example ------- The energy difference between chair and twist-boat forms for cyclohexane Force field Rel. E (kcal/mol) --------------------------- MM2 5.36 MM3 5.76 AMBER 5.82 OPLS 6.77 -Dave ******************************* * David Maxwell * * Dept. of Chemistry * * Yale University * * dave@terminus.chem.yale.edu * ******************************* From m10!frisch@uunet.UU.NET Fri May 7 10:06:21 1993 Message-Id: <9305071808.AA26605@relay2.UU.NET> Date: Fri, 7 May 93 14:06:21 EDT From: m10!frisch@uunet.UU.NET (Michael Frisch) Subject: Re: G92 and NFS To: chemistry@ccl.net Lyle Wiedeman commented: I've seen a range of opinions: * G92 wasn't meant to work through NFS * You'd be an idiot to use NFS; it's cheaper to go DIRECT * Some of us have no choice but to use NFS * G90 had bugs, but G92 is fixed * Convex G92 must be at fault, because the Sun works with the Indigo #3 is where we stand: we have G92 only one place on campus ... I should have added in my last message that point #2 is very well taken. First of all, big calculations (over 150 basis functions on any machine; over 100 basis functions on most machines) should be run direct regardless of where your disks are. If you are using a remote file system, direct is to be preferred even more strongly. Mike Frisch ------- From srheller@asrr.arsusda.gov Tue May 7 10:35:00 1993 Message-Id: <199305071835.AA04024@oscsunb.ccl.net> Date: 7 May 93 14:35:00 EDT From: "STEPHEN R. HELLER" Subject: Software/Database for review To: "chemistry" 7 May, 1993 Subject: Computer Software for Review As the Software Review Editor for the ACS Journal of Chemical Information and Computer Science (JCICS) I often get software for review in the journal. I now have some packages in hand (see below) and I am looking for people who are willing to review the software. In return for the review you get to keep the software. The review should be completed in 1-2 months. The length of the review is 4-10 double spaced typed pages. Sample reviews can be found in most of the recent issues of JCICS. I have tried this approach with some software for review in the past few months and it is working reasonably well. (For those who haven't finished your reviews of software sent a few months ago, this last sentence does not apply to you!) As a result, I am continuing this new method to find reviewers using this e- mail/user group system. I hope it continues to work. I reserve the right to abandon this if it is a problem, or inappropriate. I will not notify people if I have found a reviewer. If you don't hear from me I have chosen someone else to review the particular package. As I get many, many, (too many) replies to this message, please do not respond after 10 May (Monday), as I am sure the software will be gone by then. I can be reached on INTERNET (SRHELLER@ASRR.ARSUSDA.GOV), or if necessary, by phone at 301-504-6055 or FAX at 301-946-2704. PLEASE BE SURE TO INCLUDE AN STREET ADDRESS, PHONE and FAX NUMBER!!! (I send the software by Federal Express.) Steve Heller The packages I now have are: 1. The ACS Directory of Graduate Research (corresponding to the 1991 printed edition)on CD-ROM. A neat product. 2. Nemesis (Mac version, 2.01). Molecular Modeling sofwtare from Oxford Molecular. From jkl@OSCA.ccl.net Fri May 7 11:59:40 1993 Date: Fri, 7 May 93 15:59:40 -0400 From: Jan Labanowski Message-Id: <9305071959.AA97546@OSCA.ccl.net> To: testchem@ccl.net Subject: This is a test This test should be send via testchem It is filled with junk to pass the 100 char limit Your project balance is below the cutoff threshold, but you are allowed to continue by special permission while your new proposal is processed. Submitting a new proposal will enable you to continue using the Cray. If you have questions, contact Michele Erlenwein at 614-292-2318. ******************************************************************************