From lrellick@magnus.acs.ohio-state.edu Mon Oct 5 04:59:06 1992 Date: Mon, 5 Oct 92 8:59:06 EDT From: Lorraine M Rellick To: chemistry@ccl.net Subject: talking barbie This really takes the cake. You try to convince your kids that all scientists are not "geeks", and that being stupid is not "cool", and low and behold our largest toy manufacturer comes up with this idiot barbie doll. What is it with these people anyway? I don't understand why the media as well is constantly pushing these steriotypes. Lori Rellick, Biochemistry Dept., Ohio State University From DSMITH@uoft02.utoledo.edu Fri Oct 5 05:34:43 1992 Date: 05 Oct 1992 09:34:43 -0400 (EDT) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: Wavetracer bites the dust To: chemistry@ccl.net Wavetracer, makers of the Zephyr massively parallel box to hang on your network or MacIntosh, bit the dust on Thursday of last week. Apparently the next generation product was projected to require 15 months to reach the market and the investors said "too long" and pulled the plug. I understood that DuPont had a 16,000 processor Zephyr and really liked the speedup for fast multipole methods, dynamics, etc. Is anyone else out there sad to hear that massively parallel once again may have been within our grasp but, for computational chemistry, that day is still far away? Doug Smith Department of Chemistry The University of Toledo Toledo, OH 43606-3390 From bbesler@ouchem.chem.oakland.edu Mon Oct 5 06:49:18 1992 From: bbesler@ouchem.chem.oakland.edu (Brent H. Besler) Subject: Re: Code in Allen & Tildesley, is it on-line somewhere ? To: vamsee@abgen.tamu.edu (Vamsee Lakamsani) Date: Mon, 5 Oct 92 10:49:18 EDT The McAllen and Tildesly codes are in the pub/mtfiche directory on the anonymous FTP directory of ouchem.chem.oakland.edu(IP 141.210.108.5). I am going to put the RS 6000 Mopac 6.0 on it in a day or two as soon as I run the verification tests. From chemistry-request@ccl.net Mon Oct 5 13:01:49 1992 From: slee@hyper.com (Thomas Slee) Subject: Applying constraints on improper dihedrals in CHARMM To: chemistry@ccl.net Date: Mon, 5 Oct 1992 11:38:24 -0400 Regarding Jeffrey Nauss's question concerning Mass-Weighted Molecular Dynamics. While I cannot answer Dr. Nauss's specific question, I do have a complementary suggestion/question. Mao et al., in their Mass Weighted MD method, increase the mass by a factor of ten or so to take the system over conformational barriers easily without getting instability problems at elevated temperatures. They then have to add lots of constraints to stretches and bends etc. to prevent those modes being sampled unrealistically, (e.g., to avoid the possibility of inverting stereochemistry). My question is: what have they gained compared to simply lowering the torsional energy barriers by an appropriate factor? So far as I can see, nothing, in fact I suspect the two operations are equivalent in some sense. If I am right, then if CHARMM lets you alter torsion parameters easily, you could do so. Meanwhile, I am quite willing to be proven wrong. Any suggestions? Tom Slee, Hypercube --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net: --- everyone CHEMISTRY-REQUEST@ccl.net: --- coordinator OSCPOST@ccl.net: send help from chemistry Anon. ftp: www.ccl.net --- From R2VJV@VM1.CC.UAKRON.EDU Mon Oct 5 09:08:13 1992 Date: Mon, 05 Oct 92 13:08:13 EDT From: R2VJV@VM1.CC.UAKRON.EDU Subject: Visualization Software for IBM-RS6000 To: chemistry@ccl.net Hi netters, I am looking for a visualization software that would take x,y,z coor dinates from an MD run and render me molecules on 320H model of RISC machine. A ny 'ftp'able codes available (Like X-mol for SGi and Sun)??? Thanks in advance. venkat From R2VJV@VM1.CC.UAKRON.EDU Mon Oct 5 09:19:45 1992 Date: Mon, 05 Oct 92 13:19:45 EDT From: R2VJV@VM1.CC.UAKRON.EDU Subject: Performance of MD code on RS-6000 To: chemistry@ccl.net hi netters, I want to compare the 'performance' of my MD code on Cray-YMP to the RS-6000. Cray has a code called 'hpm' which does the performance anlysis in te rms of Mflops, instructions, etc.. Is there anything similar on RS-6000 i can u se?? I tried with the IBM representative, but did not get any replies yet. Than ks in advance. Venkat From u5949@sn2011.plk.af.mil Mon Oct 5 05:28:12 1992 From: ANDREW D. FANT Subject: MO visualization To: chemistry@ccl.net Date: Mon, 5 Oct 92 11:28:12 MDT Greetings Netters: I am in the middle of setting up a general GUI for handling quantum chemical computations on multiple remote systems. I am currently looking for pointers to programs that can do renderings of MOs and other electronic properties that are public domain or distrubuted freely. I have seen density and xmolplot, but these programs are limited by the fact that they are oriented towards one particular package and that their input formats are specialized. If you know of any generic programs that can handle this sort of task and have any personal favorites, please let me know. Either personal email or replies to the net seem in order for this question, and I will glady accept either. Thanks in advance for any insight you have. Andy +----------------------------------------------------------------------------+ Andrew D. Fant Computational Chemistry Systems Analyst TAI/UTS PLSC-Kirtland AFB fant@moe.plk.af.mil (505)266-1957 Humiston's Law: When you are surrounded by alligators, it is hard to remember your original intention was to drain the swamp. From jstewart@fai.com Sun Oct 4 16:01:51 1992 Date: Mon, 5 Oct 92 10:36:51-1795 From: jstewart@fai.com (Dr. James Stewart) To: chemistry@ccl.net Subject: Rotational Invariance in MOPAC The recent discussion in the heat of formation of benzene calculated using MNDO and AM1 interested me. Please forgive me raising this subject again; I would have commented earlier, but was incommunicado on a lecture tour, and have only just returned, complete with a bad case of jet-lag. First of all, I don't agree with anyone. Using MOPAC 6, I get the heat of formation of benzene to be about 22.02229 kcal/mol (AM1), or 21.32432 kcal/mol (MNDO). These numbers agree with the original AM1 and MNDO papers (21.2 instead of 21.3), and with the results in the PM3 paper. I could not get either 23.06206 (AM1) or 21.87987 (MNDO). Someone please explain to me how these numbers were obtained. As far as rotational invariance is concerned, great care has been taken to ensure that all calculations are rotationally invariant. Over the past nine years, I have received several papers to review in which the authors claim to have corrected faults in MOPAC which had caused loss of rotational invariance. In each case I have recommended against publication unless the authors could demonstrate that rotational invariance was lost. In a few cases, the authors withdrew their MS, and submitted it to a different Journal, where it was published. However, in no case has loss of rotational invariance ever been demonstrated. These publications caused me some grief. MOPAC has enough faults to cause users to question its soundness without them having to read articles on chimerical errors. In force constant calculations, the trivial vibration force constants and frequencies (the rotations and translations) are printed. This is to allow users to see how close the calculation came to correctly predicting these values. It would obviously be very easy to suppress these quantities, or to correct the Hessian matrix so as to ensure that the trivial modes were correct. From the discussion, I get the feeling that users would prefer not Now back to the parent issue of the fundamental constants. Yes, the constants in MOPAC 6 are outdated. They have been updated by Mr Yoshihisa Inoue, of The Green Cross Corporation, Osaka, Japan, so that in MOPAC 7 the CODATA constants will be used. This should being MOPAC into line with GAUSSIAN. Another change in MOPAC is that systems defined using Cartesian coordinates, and run using keyword XYZ, will no longer be translated and rotated. In other words, MOPAC 7 will fully support Cartesian coordinates (and SYMMETRY will have a new set of meanings when Cartesian coordinates are used). James J. P. Stewart FAX: (719) 488-9758, E-mail jstewart@fai.com From richard@TC.Cornell.EDU Mon Oct 5 10:15:41 1992 Date: Mon, 5 Oct 1992 14:15:41 -0400 From: Richard Gillilan To: chemistry@ccl.net Subject: problem with conect.f Thanks to all regarding documentation of the pdb format. Has anyone had experience with the program conect.for. It's supposed to read pdb files and create connect records for those files. It compiles on the SGI but has strange problems. A common error message is NO IMPLICIT CONNECTIVITY GENERATED FOR RESIDUE The input file is correct, I'm sure, something is going wrong with the string processing within the program. Better yet, does anyone have C code which assigns connectivity to pdb files? Thanks ----------------------------- Richard Gillilan Visualization Specialist, CNSF From zjtg05@nap.amoco.com Mon Oct 5 09:23:02 1992 Date: Mon, 5 Oct 1992 14:23:02 -0500 From: zjtg05@nap.amoco.com To: chemistry@ccl.net Subject: Barbie (Talking or otherwise) In my opinion, anyone who listens to what Barbie has to say on any subject doesn't belong in science. :Joe jtgolab@nap.amoco.com 05-Oct-92 From U09872@UICVM.bitnet Mon Oct 5 21:50:19 1992 Date: 5 October 1992 15:32:40 CDT From: "Bob Goldstein 996-6664" To: Subject: barbie doll Unfortunate though this episode with the math-phobic barbie doll is, I think art (err...toys) imitates life in this case. The social forces aligned against us geeks are far more complicated and powerful than can be embodied in one doll, no matter how popular. Does anyone actually believe that our society's fascination with thin waists and large breasts stems from Barbie's anatomical excess? The money we spend on diets and cosmetic surgery could rejuvenate more than a few labs, but a ban on Barbie would not bring those funds forthcoming. I say we should use the current flap as a reminder of how far we have to go, and let's not sound like politicians complaining about unfair media bias. Yes, the media *is* unfair, both to many politicians and to many scientists, and the unfairness does add to our problems. But the root of the problem lies elsewhere. Flames, anyone? bobg From mckelvey@Kodak.COM Mon Oct 5 17:10:12 1992 Date: Mon, 5 Oct 92 21:10:12 -0400 From: mckelvey@Kodak.COM To: osc@Kodak.COM Subject: the recent discussion concerning MOPAC The discussions on MOPAC pointed up the presence of the two values for the bohr radius. Someone pointed out differences of .01 kcal or less that were attributed to severak possible reasons. Upon changing the bohr radius to 0.529177, and the associated reciprocal I found 0.32 kcal difference in our local benchmolecule. Took 10% longer to run to the same gradient convergence criterion with .529177, etc... FYI John McKelvey E Kodak