From frits@rulglj.LeidenUniv.nl Tue Aug 23 08:40:20 1994 Received: from rulway.LeidenUniv.nl for frits@rulglj.LeidenUniv.nl by www.ccl.net (8.6.9/930601.1506) id IAA05568; Tue, 23 Aug 1994 08:18:09 -0400 Received: from rulglj.LeidenUniv.nl by rulway.LeidenUniv.nl with SMTP id AA02573 (5.65c+/IDA-1.4.4 for <@RULWAY.LEIDENUNIV.NL:chemistry@ccl.net>); Tue, 23 Aug 1994 14:17:48 +0200 Received: by rulglj.LeidenUniv.nl (920330.SGI/920502.SGI) for @RULWAY.LEIDENUNIV.NL:chemistry@ccl.net id AA26612; Tue, 23 Aug 94 14:17:35 GMT Date: Tue, 23 Aug 94 14:17:35 GMT From: frits@rulglj.LeidenUniv.nl (Frits Daalmans) Message-Id: <9408231417.AA26612@rulglj.LeidenUniv.nl> To: chemistry@ccl.net Subject: request for info on NMR spectra of organometallics Greetings, fellow CCL'ers! I have a request for information: Can any of you direct me to articles about NMR spectra of compounds of the form CH3CH2- X, with X a strong electro*positive* group (Li, Ga, etc.) or (CH3)2-CH-X (the isopropyl analogue) ? or etherate compounds (C2H5)2 O(+) X(-) We found some references, but they dated back to 1959 and the resolution of those spectra left something to wish. We don't have the equipment to synthesize these compounds ourselves, and are confident that somebody probably has spectra lying around and maybe also published them. Thanks in advance for any help, and shall I post a summary? Greetings, Frits Daalmans Frits Daalmans OIO Conformational Analysis Gorlaeus Laboratoria Leiden, The Netherlands E-mail: frits@rulglj.leidenuniv.nl Tel: [+31] (0)71-274505 From grzesb@asp.biogeo.uw.edu.pl Tue Aug 23 09:40:26 1994 Received: from asp.biogeo.uw.edu.pl for grzesb@asp.biogeo.uw.edu.pl by www.ccl.net (8.6.9/930601.1506) id JAA06740; Tue, 23 Aug 1994 09:20:28 -0400 Received: by asp.biogeo.uw.edu.pl (5.61/1.34) id AA07017; Tue, 23 Aug 94 16:17:43 +0200 Date: Tue, 23 Aug 94 16:17:43 +0200 From: grzesb@asp.biogeo.uw.edu.pl (Grzegorz Bakalarski) Message-Id: <9408231417.AA07017@asp.biogeo.uw.edu.pl> To: chemistry@ccl.net Subject: DMOL: Does exist v. 2.35 for CRAY ? Dear CCL, I'd like to ask if anyone of you has ever used (or seen) DMol version 2.35 on CRAY computer system. (DMOL is a DFT program from Biosym, San Diego). We have version 2.3 which has some serious bugs ( e.g. LYP functional). This version was "new" in the end of 1992 (we got it then running on workstation). Lately, for some period I have used v. 2.35 running on SGI and I have got several good results using LYP and new minimizer (quite good). But I need it running on big machine, because I plan to investigate big molecular systems ( about 50 atoms). So, please send me any information about new (!) version of DMOL for CRAY (if exist - how is its performance; if not exist - when will it be available (if ever). Thanks in advance. Best wishes, Grzegorz From LIPNICK.ROBERT@epamail.epa.gov Tue Aug 23 09:45:44 1994 Received: from VAXTM1.RTPNC.EPA.GOV for LIPNICK.ROBERT@epamail.epa.gov by www.ccl.net (8.6.9/930601.1506) id JAA06752; Tue, 23 Aug 1994 09:21:39 -0400 Received: from pyxis.rtpnc.epa.gov by epavax.rtpnc.epa.gov (PMDF V4.3-7 #5309) id <01HG8RQVGMEO8X3ZMA@epavax.rtpnc.epa.gov>; Tue, 23 Aug 1994 09:10:11 EDT Received: from mr.rtpnc.epa.gov by mail.rtpnc.epa.gov (PMDF V4.3-7 #5309) id <01HG8RIFUYCG8Y6RBG@mail.rtpnc.epa.gov>; Tue, 23 Aug 1994 09:05:08 EDT Received: with PMDF-MR; Tue, 23 Aug 1994 09:00:32 EDT MR-Received: by mta CARINA; Relayed; Tue, 23 Aug 1994 09:00:32 -0400 Alternate-recipient: prohibited Disclose-recipients: prohibited Date: Tue, 23 Aug 1994 08:44:00 -0400 (EDT) From: ROBERT LIPNICK 202-260-1274 Subject: RE: CCL:Linus Pauling To: chemistry-request Cc: shenkin , stoutepf , chemistry , stoutepf Message-id: <01HG8RM0WE2A8Y6RBG@mr.rtpnc.epa.gov> X-Envelope-to: chemistry-request@ccl.net, chemistry@ccl.net MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Posting-date: Tue, 23 Aug 1994 09:00:00 -0400 (EDT) Importance: normal Priority: normal X400-MTS-identifier: [;23009032804991/1561532@MAIL] A1-type: MAIL Hop-count: 1 I recall the same kind of response from Linus Pauling on a TV interview (I think it was PBS). He was asked how he had so many good ideas and said something like I start out with a very large number of ideas and throw away the ones that are not so good. Several years ago I was a participant in arranging for a short "living history" videotape of him by the Wood Library Museum of Anesthesiology in which he was interviewed about the clathrate theory of anesthesia that he had proposed. +-----------------------------EPA---------------------------+ | US Environmental Protection Agency | | Office of Pollution Prevention and Toxics (Mailstop 7403) | | 401 M Street, SW, Washington, DC 20460 USA | | TEL: 202-260-1274; FAX: 202-260-1236 or 202-260-1283 | | EMAIL: lipnick.robert@epamail.epa.gov | | Robert L. Lipnick, Ph.D., Senior Chemist (QSAR-Toxicology)| +----------------------------EPA----------------------------+ From bradt@gac.edu Tue Aug 23 11:43:02 1994 Received: from gac.edu for bradt@gac.edu by www.ccl.net (8.6.9/930601.1506) id KAA09458; Tue, 23 Aug 1994 10:54:39 -0400 Received: by gac.edu (NeXT-1.0 (From Sendmail 5.52)/GAC-1.0.R9309061) id AA19995; Tue, 23 Aug 94 09:54:37 CDT Date: Tue, 23 Aug 94 09:54:37 CDT From: bradt@gac.edu (Brad Thompson) Message-Id: <9408231454.AA19995@gac.edu> To: CHEMISTRY@ccl.net Subject: experimental geometry Adel El-Azhary writes: > Can someone elaborate on the difference of the geometry by microwave, > electron diffraction and X-Ray. Can you give references. My ynderstanding > is that the microwave geometry is better than the others but I do not know > exactly why. What's "better" depends on the molecule and what information you want. First off, ED and XRay give you gas-phase, i.e. isolated molecule, info, which may or may not be what you want. Also, neither can handle large species. When both ED and MW can give you a structure, bond distance differences are likely to be at the .00x Angstrom level. It's important to remember vibrational amplitudes are .0x Angstroms! Both ED and MW measure some sort of average distance, and just what average that is depends both on the experimental method and on the way the distances were deduced from the data. And common methods of data treatment, for both ED and MW, can go pathological in the hands of the naive or careless user. [But of course, that sort of thing never happens to theorists. :) ] So in terms of the real world and the measurements we can make on it, all those digits (past, say, .01 Angstrom and 1 degree) in geometries we get from Gaussian 92 don't have a lot of significance. There's an extensive literature on just what ED and MW distances "mean." I really don't recommend it to those outside the fields unless you badly need to know! | H. Bradford Thompson [Brad] bradt@gac.edu | Scholar in Residence, Chemistry & Physics | Gustavus Adolphus College, St. Peter MN 56082-1498 From mizan@engin.umich.edu Tue Aug 23 11:46:33 1994 Received: from rom.engin.umich.edu for mizan@engin.umich.edu by www.ccl.net (8.6.9/930601.1506) id LAA10698; Tue, 23 Aug 1994 11:39:47 -0400 Received: (mizan@localhost) by rom.engin.umich.edu (8.6.8/8.6.4) id LAA25067 for CHEMISTRY@ccl.net; Tue, 23 Aug 1994 11:39:46 -0400 Date: Tue, 23 Aug 1994 11:39:46 -0400 From: "Tahmid I. Mizan" Message-Id: <199408231539.LAA25067@rom.engin.umich.edu> To: CHEMISTRY@ccl.net Subject: SUMMARY:predictor-corrector/quaternion for SPC Thanks to everybody who responded to my question regarding the predictor- corrector/quaternion method as appled to SPC water. The quaternion method, of course, unlike SHAKE, solves the rigid body equations of motion for the molecule as a whole. Analytic stability analysis of MD equations is not possible. Some sort of approximate analysis may be possible by linearizing the differential equations or by Lyapunov methods. I did not attempt this, but rather took a trial-and-error approach. It turns out that for 2 fs or larger time step, iterating on the evaluation-correction step solves the problem. Of course, this means an extra force evaluation per time-step which is undesirable. However, for 3 fs timestep a P(EC)**2 (two force evaluations per time step) appears to be stable so that there is some computational advantage over a 1 fs time-step ( 0.67 force evaluations per fs as opposed to 1 force evaluation per fs). The 3 fs runs give the correct values of all static properties ( I have not calculated autocorrelation functions). I should mention that for a 4 fs time step, the situation deteriorates and a P(EC)**3 is required for stability. T. I. Mizan University of Michigan ******************************************************************************* ORIGINAL QUESTION I am using the predictor-corrector/quaternion subroutines from Allen & Tildesley to simulate SPC water. When I use a 1 femtosecond timestep the program runs properly and gives the correct results for energy, pressure g(r) etc. However, when I use a 2 fs timestep the program 'blows up'. Apparently the OH bond lengths become larger and larger and it just blows up. So it appears to be some kind of numerical instability. Has anybody else had a similar experience ? Or is it just some error in my implementation. Is there a fix ? -- Tahmid Mizan ******************************************************************************* From steve@chem.columbia.edu Tue Aug 16 21:21:04 1994 Perhaps I can answer your questions about your water dynamics. I also do simulations of SPC water, although not with predictor-corrector, or quaternions. So I can't say whether there's a bug in Allen & Tildesley's code. But timesteps of 1-2 femtoseconds are about as large as you can usually use on rigid water. Some people use as high as 2 fs, I can't go any higher than 1 fs, but it depends a little on your algorithm. So this makes it sound like it's not a bug but just an instability at large timesteps. But the fact that your OH bond(s) keep growing makes it sound like there might be some other problem. That isn't the sort of blowup I'd expect from timesteps, although I haven't used quaternions, so I could be mistaken. Hope this helped. -Steve Stuart steve@chem.columbia.edu ******************************************************************************* From ross@cgl.ucsf.EDU Tue Aug 16 21:21:14 1994 Are you using SHAKE on your water bonds? It seems to be necessary with models that use a larger O vdw to enclose the H's, because the margin of coverage for the H charges is too small for bond stretching to be acceptable w/ longer time steps. Bill Ross ******************************************************************************* From d3f012@pellucidar.pnl.gov Wed Aug 17 00:01:02 1994 Tahmid, Are you constraining the geometry of the water molecule (bond and angle) with SHAKE? With SPC, your hydrogens have no lennard-jones terms and but they do have charge. If you don't constrain these hydrogens they can easily cause your calc. to blow up. Mark Mark A. Thompson Sr. Research Scientist email: d3f012@pnlg.pnl.gov Molecular Science Research Center FAX : 509-375-6631 Pacific Northwest Laboratory voice: 509-375-6734 PO Box 999, Mail Stop K1-90 Richland, WA. 99352 ******************************************************************************* From kdb@oddjob.uchicago.edu Wed Aug 17 01:50:59 1994 Hello I am responding to your question about stability of A&T algorithm for water. Although I have not worked with this, my officemate has, but is in taiwan until the end of the month. If you are still interested in comunicating with him, his e-mail is feng@cloister.uchicago.edu (his name is Felix Li) Hope this little bit helps... Keith Ball U of C physics grad ******************************************************************************* From ruusvuor@csc.fi Wed Aug 17 03:41:07 1994 Hello Tahmid, In the case of the Verlet algorithm and nonbonded atoms the blowing up is a typical behaviour when the time step is increased. See for example the User Guide, Part 1 for Discover 2.9/3.1, January 1993, Biosym, pp. 1/2-58 - 1/2-61: As the two nonbonded atoms approach each other and the time step is long they may "deeply interpenetrate each other's steeply repulsive wall between steps. The resulting force is now so large that the atoms fly off at a speed about 1 A/fs (or 10^5 m/s). An equivalent temperature would be in the hundreds of thousands of degrees". If a Morse potential is used for the bond-streching term in the forcefield also the bonded atoms probably behave by this way, because this potential allows the bonded atoms to drift unrealistically far apart. If you are using harmonic potentials then I don't know what happens. There is some discussion about possible errors in a MD program in the Section 3.5 "Check on accuracy" (pp. 98-101) in the Allen & Tildeslay's book "Computer Simulations of Liquids" Regards, Raimo ------------------------------------------------------------------------ Raimo Uusvuori | Phone: +358-0-457 3210 Scientific Software Specialist | FAX: +358-0-457 2302 Chemistry | | Center for Scientific Computing | Street address: P.O. Box 405 | Tietotie 6, FIN-02150 ESPOO FIN-02101 ESPOO | E-mail: ruusvuor@csc.fi FINLAND | Raimo.Uusvuori@csc.fi ------------------------------------------------------------------------ ******************************************************************************* From matro@haydn.chm.uri.edu Wed Aug 17 09:16:40 1994 This is in reply to your question about 1 vs 2 fs timesteps. I assume you are talking about the integration timestep. I think 2 fs is getting too long for a timestep in water since the vibrational period of the highest-frequency normal mode is about 9 fs (3756 cm-1) If you increase the timestep further, does the program still blow up? does it work if you decrease the timestep below 1 fs? Hope this helps, Alex Matro ******************************************************************************* From topper@magnum.cooper.edu Wed Aug 17 09:24:21 1994 With regards to your recent posting to the CCL: I think that the predictor-corrector/quaternion subroutines you are using are guaranteed to exhibit the kind of numerical instability you have observed when the timestep is "too large." How large "too large" is will depend entirely on the system you are modeling (a timestep for water might be overkill for handling, say, liquid argon). This is based on limited experience (i.e., I haven't implemented the subroutines in Allen/Tildesley you are using). I will be interested to hear if someone tells you differently. Best wishes! robert topper Prof. Robert Q. Topper internet: topper@cooper.edu Department of Chemistry phone: (212) 353-4378 The Cooper Union FAX: (212) 353-4341 Cooper Square subway: take the N/R to 8th/NYU New York, NY 10003 USA or the 6 to Astor Place The Cooper Union for the Advancement of Science and Art, established by Peter Cooper in 1859, is a private institution of higher learning where all students receive full-tuition scholarships. ******************************************************************************* From khalid.mansour@srs.gov Wed Aug 17 12:11:45 1994 Tahmid, I would like to have some info on the SPC water model. Will you please provide some References? Thanks. By the way, I do not know if my answer is too simplistic, but it appears to me that P/C quaternion is unstable at 2 fs , so then your total energies and other vbles go crazy (no Energy conservation, I'll suspect). Play with it from 0.5 fs to 1.5 fs and see if you get conservation of E. (for example at if you run 150 steps at 0.5 fs it should match the energy at the 50 th step of the 1.5 fs, if it does NOT, then 1.5 fs is NO GOOD, andso forth). Let me know how it goes regards, khalid ******************************************************************************* From ryszard@MSI.COM Mon Aug 22 18:19:16 1994 Dear Tahmid, Do you know what is the maximum allowable time step for the integrator you are using ? Note that most probably the method you are using is only "conditionally stable" i.e. stable for small time step and unstable for time step grater then certain treshold. For more detail analysis you may refer any handbook devoted to MD and/or numerical solutions for differential equations e.g. J.M. Haile "Molecular Dynamics Simulation: Elementary Methods" J. Wiley & Sons, Inc. and most probably Allen & Tildesley as well. Of course this does not exclude possibility of the bug in your implementation - unfortunately. Sincerely, Ryszard Czerminski, MSI ******************************************************************************* ------- Regard Tahmid Mizan From sxj23@slc8.INS.CWRU.Edu Tue Aug 23 12:40:24 1994 Received: from slc8.INS.CWRU.Edu for sxj23@slc8.INS.CWRU.Edu by www.ccl.net (8.6.9/930601.1506) id LAA10988; Tue, 23 Aug 1994 11:46:15 -0400 Received: (sxj23@localhost) by slc8.INS.CWRU.Edu (8.6.8.1+cwru/CWRU-2.1-freenet) id LAA19639; Tue, 23 Aug 1994 11:46:12 -0400 (from sxj23) Message-Id: <199408231546.LAA19639@slc8.INS.CWRU.Edu> Date: Tue, 23 Aug 1994 11:46:12 -0400 From: sxj23@po.CWRU.Edu (Shu-Chuan Jao) To: chemistry@ccl.net Subject: UNIX - rm Reply-To: sxj23@po.CWRU.Edu (Shu-Chuan Jao) Hi! I am really in a big trouble. I accidentally typed "rm *" and, as you can image, all my files in that directory are gone. We did not do backup. So, I cannot restore those files. I know that there are some packages that can do "undelete" on DOS to recover files which are deleted. Is there package doing the same thing for unix? I appreciate any responds. 08/23/94 -- o-----------------------------------------------------------------o | Shu-Chuan Jao (Chris) TEL : 216-368-4476 | | E-mail : sxj23@po.cwru.edu OR chrissie@laurel.chem.cwru.edu | o-----------------------------------------------------------------o From rudolphc@sbh.Cyanamid.COM Tue Aug 23 13:40:24 1994 Received: from pt.Cyanamid.COM for rudolphc@sbh.Cyanamid.COM by www.ccl.net (8.6.9/930601.1506) id NAA13159; Tue, 23 Aug 1994 13:13:06 -0400 Received: by sbh.Cyanamid.COM (931110.SGI/911001.SGI) for @igate.cyanamid.com:chemistry@ccl.net id AA00926; Mon, 23 Aug 93 19:12:01 +0200 Date: Mon, 23 Aug 93 19:12:01 +0200 From: rudolphc@sbh.Cyanamid.COM (Christine Rudolph) Message-Id: <9308231912.ZM924@sbhx02.sbh.Cyanamid.COM> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: Help for modelling B-O compounds Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Dear netters, is anybody out there who has got experience with modelling organic compounds containing B-O bonds? SYBYL parameters or hints concerning atomic partial charges would be very helpful. I'll summarise. Thanks in advance, Christine Rudolph -- ================================================================================ Dr. Christine Rudolph phone: ++49 - 6130 - 911 - 403 Molecular Modelling fax: ++49 - 6130 - 911 - 113 Cyanamid Forschung GmbH e-mail:rudolphc@sbh.cyanamid.com Zur Propstei 55270 Schwabenheim Germany ================================================================================ From theochem@ctc.com Tue Aug 23 13:41:52 1994 Received: from server1.ctc.com for theochem@ctc.com by www.ccl.net (8.6.9/930601.1506) id MAA12892; Tue, 23 Aug 1994 12:59:44 -0400 Received: by server1.ctc.com (5.65/DEC-Ultrix/4.3) id AA26672; Tue, 23 Aug 1994 13:01:09 -0400 Received: by eed02.ctc.com (920330.SGI/921111.SGI.AUTO) for @server1.ctc.com:chemistry@ccl.net id AA00490; Tue, 23 Aug 94 12:58:20 -0400 From: theochem@ctc.com (Douglas Smith) Message-Id: <9408231658.AA00490@eed02.ctc.com> Subject: Biosym mailing list? To: chemistry@ccl.net (Computational Chemistry List) Date: Tue, 23 Aug 1994 12:58:08 -0500 (EDT) X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1399 I have looked through the CCL archives for information on a Biosym users mailing list and/or interest group. I found a year old message from Phil Kutzenco about the mail reflector dibug. Is this the only list, or are there others? Doug -- Douglas A. Smith Theoretical Chemist Concurrent Technologies Corporation 1450 Scalp Avenue Johnstown, PA 15904 voice: (814) 269-2545 fax: (814) 269-2798 email: theochem@ctc.com !!!NEW!!! Stadnard Disclamur: All opinions, comments, mistakes, endorsements and odd noises are my own, not my employer's. and still: Douglas A. Smith voice: N/A Associate Professor fax: N/A Department of Chemistry email: dsmith@uoft02.utoledo.edu and Center for Drug Design and Development The University of Toledo Toledo, OH 43606-3390 +---------------------------------+---------------------------------+ | "The juvenile sea squirt wanders through the sea searching for | | a suitable rock or hunk of coral to cling to and make its home | | for life. For this task it has a rudimentary nervous system. | | When it finds its spot and takes root, it doesn't need its | | brain any more so it eats it. It's rather like getting tenure." | | --source unknown | +-------------------------------------------------------------------+ From bkarlak@ren.onyx-pharm.com Tue Aug 23 15:40:41 1994 Received: from iserver.onyx-pharm.com for bkarlak@ren.onyx-pharm.com by www.ccl.net (8.6.9/930601.1506) id PAA15759; Tue, 23 Aug 1994 15:12:50 -0400 Received: from ren.onyx-pharm.com by iserver.onyx-pharm.com (5.67/1.37) id AA22356; Tue, 23 Aug 94 12:12:49 -0700 Received: by ren.onyx-pharm.com (931110.SGI/921111.SGI.AUTO) for @iserver.onyx-pharm.com:chemistry@ccl.net id AA11984; Tue, 23 Aug 94 12:12:47 -0700 Date: Tue, 23 Aug 94 12:12:47 -0700 From: bkarlak@ren.onyx-pharm.com (Brian Karlak) Message-Id: <9408231912.AA11984@ren.onyx-pharm.com> To: chemistry@ccl.net Subject: Mac SMILES converter. Hi y'all - Does anyone out there know of a program or method to batch convert SMILES to .PICT files of 2D structures? Thanks! Brian Karlak Onyx Pharmaceuticals "For I am a cat, and since when has a cat given anyone a straight answer?" From rlr@acsu.buffalo.edu Tue Aug 23 17:40:25 1994 Received: from autarch.acsu.buffalo.edu for rlr@acsu.buffalo.edu by www.ccl.net (8.6.9/930601.1506) id RAA19005; Tue, 23 Aug 1994 17:16:50 -0400 Received: (rlr@localhost) by autarch.acsu.buffalo.edu (8.6.8/8.6.4) id RAA23293 for CHEMISTRY@ccl.net; Tue, 23 Aug 1994 17:16:45 -0400 Date: Tue, 23 Aug 1994 17:16:45 -0400 From: "Raymond L. Roskwitakski" Message-Id: <199408232116.RAA23293@autarch.acsu.buffalo.edu> To: CHEMISTRY@ccl.net Subject: Dose Biosym help exists ??? Content-Length: 216 Does anyone know of an email address or 1-800-number for Biosym 's Delphi, and other software packages (Insight, Discover, Homology, etc). Thanks in advance. Raymond Roskwitalski, Jr. rlr@autarch.acsu.buffalo.edu From bradt@gac.edu Tue Aug 23 19:40:28 1994 Received: from gac.edu for bradt@gac.edu by www.ccl.net (8.6.9/930601.1506) id SAA20078; Tue, 23 Aug 1994 18:49:25 -0400 Received: by gac.edu (NeXT-1.0 (From Sendmail 5.52)/GAC-1.0.R9309061) id AA00827; Tue, 23 Aug 94 17:49:23 CDT Date: Tue, 23 Aug 94 17:49:23 CDT From: bradt@gac.edu (Brad Thompson) Message-Id: <9408232249.AA00827@gac.edu> To: CHEMISTRY@ccl.net Subject: experimental geometry (correction) Sorry. In my message on "exerimental geometry" this morning I said: > What's "better" depends on the molecule and what information you want. > First off, ED and XRay give you gas-phase, i.e. isolated molecule, info, > which may or may not be what you want. Also, neither can handle large > species. I meant to say, ... ED and MW, in contrast to XRay, give you gas-phase, i.e., isolated molecule, info. .... A classic case of the fingers getting behind the brain. Thanks to Gary Newton for calling this to my attention promptly. | H. Bradford Thompson [Brad] bradt@gac.edu | Scholar in Residence, Chemistry & Physics | Gustavus Adolphus College, St. Peter MN 56082-1498 From jmeehan@cc.utas.edu.au Tue Aug 23 19:42:42 1994 Received: from corinna.its.utas.edu.au for jmeehan@cc.utas.edu.au by www.ccl.net (8.6.9/930601.1506) id SAA20092; Tue, 23 Aug 1994 18:53:19 -0400 Received: from tasman.cc.utas.edu.au by corinna.its.utas.edu.au with SMTP id AA21124 (5.67a/IDA-1.5 for ); Wed, 24 Aug 1994 08:52:53 +1000 Date: Wed, 24 Aug 1994 08:50:42 +1000 (EST) From: John Meehan Subject: Re: CCL:UNIX - rm To: Shu-Chuan Jao Cc: chemistry@ccl.net In-Reply-To: <199408231546.LAA19639@slc8.INS.CWRU.Edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 23 Aug 1994, Shu-Chuan Jao wrote: > Hi! I am really in a big trouble. I accidentally > typed "rm *" and, as you can image, all my files in > that directory are gone. We did not do backup. So, I > cannot restore those files. I know that there are some > packages that can do "undelete" on DOS to recover files > which are deleted. Is there package doing the same thing > for unix? > I appreciate any responds. 08/23/94 This was posted to comp.archives a little while ago. It may help.... >X-Url: ftp://gatekeeper.dec.com/pub/sysadm/recover.tar.Z Archive-Name: auto/comp.unix.admin/File-recovery-program Below is a "Dr. File System" article I wrote as commentary on possible solutions to the problem of recovering lost files on UNIX systems, especially those using the Berkeley Fast File System. The article observes that it should be possible to write a program which examines the cylinder group free fragment bit maps. Once you have the bit maps, it is fairly easy to read the free blocks of the file system and examine the old data in them. A few months ago I removed some program sources that hadn't been backed up yet and were long enough I didn't want to type them in again. So, I wrote the program loosely described by the article. Having been careful not to disturb the free list of the disk while writing this program, I got back the previous sources. More recently, I dusted off the program, updated it to run on DEC OSF/1 and fixed the stupidly slow parts to go faster. A compressed archive of the program has been placed on: gatekeeper.dec.com:/pub/sysadm/recover.tar.Z Enjoy. If you have any questions about it, send me mail at "alan@nabeth.cxo.dec.com". Alan Rollow alan@nabeth.cxo.dec.com * * * Dear Dr. File System, I just typed "rm -r" by accident in the wrong place and all my files are gone. How do I get them back? Oh, by the way. I don't have any backups... signed, Clueless Dear Clueless, You stupid twit! [ and off Dr. File System goes into his usual rant about not keeping good backups... ] * * * While Dr. File System is ranting, perhaps we can help Clueless with his problem (and make a bundle of money off software consulting services in the process). First examine what rm(1) really does: Process the argument list, making note of which options are used. For all remaining arguments, if the argument is ".." continue. Otherwise "remove" it. "Removing" consists of taking care of details like not being able to remove directories, except as part of a recursive remove, making sure the file is really there, etc. In the end, it comes down to doing an unlink(2) on the filename. The unlink(2) system call removes the file's name and inode number from the directory and decrements the link count. It is worth pointing out for those that didn't know it already that a file can have many names, but only one inode. The inode includes a reference count of how many names it has. These references are also called hard links. When the link count goes to zero AND the file is no longer open, then the file is removed. Thus it is possible to create a file, unlink it (removing the name) and let the opening processes continue to use it. When the file is closed or the process exits, the file goes away. Actually getting rid of the file consists of putting the blocks it was using back on the "free list" and clearing the inode. For the fast file system this "free list" is actually a bit map for each cylinder group. A simple system macro is used to calculate the cylinder group number from the block number. It's also worth noting that neither rm(1) nor the file system do anything with the contents of the block when it removes the file or puts the block on the "free list". Using this collection of information it may be possible to help Clueless recover some of his data. The first, absolute most important thing to do is make sure the file system changes as little as possible. This may require rather extreme measures (like shutting down or crashing the system). The point of this is to prevent the blocks that were part of Clueless' files from getting allocated to other users. Making a PHYSICAL backup of the partition holding the file system is a good idea. This will let the recovery operate on a copy of the data, while returning the disk to the service of the people that might be using it. Now to the recovery. First, recall that the inodes were cleared when the files were removed. If they hadn't been, it would be fairly simple matter to examine all the free inodes to determine which had been owned by Clueless and look at the block lists to determine where the data was. This avenue isn't available to us, though. What remains is the examination of the data on the disk in the hopes of picking out the pieces that were part of Clueless' files and putting them back together like many jigsaw puzzles. The methods for this examination can vary from brute force approach to a highly optimized one. Consider the choices. 1. Theme - Examine every LBN of the disk. Pick out the LBNs that were probably interesting and ignore the rest. This has the disadvantage of not throwing out blocks allocated to other people and those that are part of the file system's data structures. 2. Variation #1 - Observe that the Fast File System is organized in pieces of data having two sizes; the fragment and the file block size. Depending on the allocation scheme only the block size may be interesting. The only advantage this has over the Theme is that there are few blocks to examine. 3. Variation #2 - The skilled mechanic can easily identify what file system block belong to the file system overhead and what blocks are data. This is bound to help some. 4. Variation #3 - Observe that only free blocks are likely to contain Clueless' data. Each cylinder group has a bit map of the free space for that cylinder group. If the skilled mechanic is able to filter out the file system overhead, then limiting the search to the free list, shouldn't be that much harder. 5. Variation #4 - The value of this optimization depends on exactly what Clueless removed and how the files were arranged. If the files were in a directory and only the file in that directory were removed (no subdirectories), then we can make a good guess where to start the search. Recall from previous discussions that when a file is created it prefers to end up in the same cylinder group as the directory in which it resides. If you can determine what cylinder group the directory of interest is in, then you can start the search in that cylinder group. While you may still have to search all the cylinder groups to find all the data, there is a chance that you can recover an interesting amount of the quickly. A program to do such a search is not exceeding difficult with enough study of the file system include files and a good starting example. A good version of the program would perform some data analysis of each block in the hopes of identifying it. Sort of like file(1). A further enhancement would allow formatting the data in various ways, like od(1). All of the interesting recovery work is the examination of the data, not getting the data to examine. -- Alan Rollow alan@nabeth.cxo.dec.com ---------------------------------------------- John Meehan O CH2-COOH Department of Biochemistry " / University of Tasmania, HO-P-O-C-COOH Australia | \ HO CH2-COOH PHOSPHOCITRIC ACID ---- A powerful, natural inhibitor of Pathological Biomineralization ---------------------------------------------- From ascanio@salve3.salve.edu Tue Aug 23 22:40:29 1994 Received: from SALVE3.SALVE.EDU for ascanio@salve3.salve.edu by www.ccl.net (8.6.9/930601.1506) id WAA22590; Tue, 23 Aug 1994 22:12:39 -0400 From: Received: by salve3.salve.edu (MX V3.2) id 9642; Tue, 23 Aug 1994 22:14:11 EDT Date: Tue, 23 Aug 1994 22:14:10 EDT To: chemistry@ccl.net Message-ID: <0098365C.C3960660.9642@salve3.salve.edu> Subject: Linus Pauling/Marie Curie Linus Pauling is indeed the only MAN to be awarded two Nobel Prizes in two different categories(Chemistry and Peace). Marie Curie is the only person to be awarded two Nobel Prizes in two different categories of Science( Chemistry(1903) and Physics(1911 ?) with husband Pierre). John Bardeen did it the easy way - both in Physics. Pacem in Calcio /////////// |/////| | 3 | Ascanio Giuseppe DiPippo, C.H.S.,C.A.O.S. ////// / liter \ Salve Regina University ___ |//| / \ Newport, Roe Dylin 02840 ___| |__ / \ | et cum | ascanio@salve3.salve.edu |___ ___| | H2O | | spiriti | 401-847-6650 | | | | | vini | 41 30'N 71 20'W |__| -------- -------------- **************************************************************** * " Neva trusst n nee won whoo kan ownly spel a wird won whey" * ******************** Mock Twane ********************************  From bear@ellington.pharm.arizona.edu Tue Aug 23 22:43:56 1994 Received: from ellington.pharm.arizona.edu for bear@ellington.pharm.arizona.edu by www.ccl.net (8.6.9/930601.1506) id WAA22596; Tue, 23 Aug 1994 22:12:45 -0400 Received: by ellington.pharm.arizona.edu (931110.SGI/920502.SGI) for chemistry@ccl.net id AA07856; Tue, 23 Aug 94 19:12:10 -0700 Date: Tue, 23 Aug 94 19:12:10 -0700 From: bear@ellington.pharm.arizona.edu (Soaring Bear) Message-Id: <9408240212.AA07856@ellington.pharm.arizona.edu> To: chemistry@ccl.net Subject: CCL: Biosym mailing list? >Douglas Smith (theochem@ctc.com) wrote:) >I have looked through the CCL archives for information on a Biosym users >mailing list and/or interest group. I found a year old message from >Phil Kutzenco about the mail reflector dibug. Is this the only list, or are >there others? Dibug is the only Biosym user group. It was founded by Peter Shenkin Oct 1990. Subscription and archive addresses are at bottom of this message. Archive also available by Mosaic via URL: Biosym, Dibug However, dibug was suspended by the reflector maintainer with this message. From doelz@comp.bioz.unibas.ch Tue Aug 16 01:10:44 1994 From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: Terminating the conversation Colleagues, Whilst I appreciate that the DIBUG list was and hopefully will become again a forum of scientific exchange, I have observed the mails which showed up during by vacation with some concern. There wasn't only the 'self-submitting' vacation job which looped (similar event is current- ly blasting another mailing list I am subscribed to) but these issues on BIOSYM documentation with emotional flair really help nothing. It might have been appropriate to state what has been said with a chain of examples which should be a lead to improve, but banging the issue over and over again is in noone's interest. I thought that it might fade out without my interference but seeing it come up again is frus- trating enough to take action. In order to cool down, the mail subscription will be stopped until September 15, in order to allow for a month's recovery. You will stay subscribed but the mail messages will not be forwarded to the members of the list. Please refer from resuming the discussion after September 15. If you dislike my action I am perfectly prepared to have someone else main- tain the list but I would request measures to have these endless flame wars stop. ==================================================================== THIS LIST WILL BE SUSPENDED FROM OPERATION UNTIL SEPTEMBER 15. BUGS AND MESSAGES TO BIOSYM SHOULD BE ADDRESSED, AS BEFORE, TO THE APPRO- PRIATE BIOSYM EMAIL ADDRESS. WE WILL ALLOW FOR REDISTRIBUTION AGAIN AT SEPTEMBER 15 BUT CLOSE THE LIST ENTIRELY IF FLAME WARS CONTINUE. ==================================================================== I apologize for the need to act as censor in this situation but we have been operating DIBUG voluntarily in the past years, with the ambition to provide a forum of scientific discussion. This is no longer the case. Please consider the originators of the emotional arguments to be the reason for the trouble, and refer from flaming. Regards Reinhard Doelz Head, Biocomputing Biozentrum der Universitaet Basel +---------------------------+-------------------------------------------+ | Dr. Reinhard Doelz | Tel. x41 61 2672247 Fax x41 61 2672078 | | Biocomputing | electronic Mail doelz@urz.unibas.ch | |Biozentrum der Universitaet+-------------------------------------------+ | Klingelbergstrasse 70 | EMBnet embnet@ch.embnet.org | |CH 4056 Basel SWITZERLAND | Switzerland gopher.embnet.unibas.ch | +---------------------------+------------- http://beta.embnet.unibas.ch/ ____________________________________________________________________________ The following information is automatically appended by the mailer. This list is called DIBUG@COMP.BIOZ.UNIBAS.CH and covers the Discover, Insight and Biosym products User group. Mail (un)subscribe messages to DIBUG-REQUEST@COMP.BIOZ.UNIBAS.CH, other to DIBUG-ADMIN@COMP.BIOZ.UNIBAS.CH The archive is available on bioftp.unibas.ch as FTP and GOPHER service. * UU UU SOARING BEAR * * UU UU Computer Aided Drug Design * * UU UU A University of Arizona, New Pharmacy 404 * * UUUU AAA Tucson, AZ 85721 602-626-6133 * * AA AA where the sun shines * * AAAAAAA * * AA AA e-mail:bear@ellington.pharm.arizona.edu * From wtwinter@mailbox.syr.edu Tue Aug 23 23:40:32 1994 Received: from SUVM.SYR.EDU for wtwinter@mailbox.syr.edu by www.ccl.net (8.6.9/930601.1506) id XAA22921; Tue, 23 Aug 1994 23:00:21 -0400 Received: from mothra.syr.edu by SUVM.SYR.EDU (IBM VM SMTP V2R2) with TCP; Tue, 23 Aug 94 23:01:24 LCL Received: by mothra.syr.edu (4.1/Spike-2.0) id AA27821; Tue, 23 Aug 94 22:57:02 EDT Date: Tue, 23 Aug 1994 22:57:01 -0400 (EDT) From: "William T. Winter" Subject: Re: CCL:experimental geometry To: Brad Thompson Cc: CHEMISTRY@ccl.net In-Reply-To: <9408231454.AA19995@gac.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 23 Aug 1994, Brad Thompson wrote: ,> What's "better" depends on the molecule and what information you want. > First off, ED and XRay give you gas-phase, i.e. isolated molecule, info, > which may or may not be what you want. Also, neither can handle large > species. Not so! electron diffraction, historically, was a gas phase technique but there is an expanding literature of crystal structures determined by electron diffraction. X-ray diffraction is the classical approach for studying molecular structure in a macroscopic crystal and has been widely applied to proteins, nucleic acids, other natural and synthetic polymers and a huge range of other crystalline materials. > > When both ED and MW can give you a structure, bond distance differences > are likely to be at the .00x Angstrom level. It's important to remember > vibrational amplitudes are .0x Angstroms! Both ED and MW measure some > sort of average distance, and just what average that is depends both on > the experimental method and on the way the distances were deduced from the > data. Don't all experimental methods average over the sample in some manner? A more important point is that the time and sample averaged structure in a crystal lattice (XRD and ED) need not be identical to the time and space averaged structure in any other phase or even in a different crystalline polymorph. One further key difference is that the atomic form factors used to describe scattering of x-rays by atoms increase with increasing atomic number. Thus positions of hydrogen atoms in hydroxyl groups are often impossible to define due to a combination of weak scattering power and mobility of the atom within the structure. As in any experimental method the uncertainties in derived results depend upon the number and quality of the data. In well-determined crystal structures the esd s in bond lengths is often less than 0.001 Angstrom while that in bond angles is in the 0.x degree region. If one attempts to average geometries over a family of related compounds the esds increase to 0.001-3 angstrom and the esd in bond angles is 0.5 - 1.5 degrees. A number of such studies on various structure families were done in the 1970's and 80's. For better crystal data on distances involving hydrogen atoms one should look at the neutron diffraction literature, since neutron diffraction intensities are quite sensitive to hydrogen atom coordinates. ... > There's an extensive literature on just what ED and MW distances "mean." > I really don't recommend it to those outside the fields unless you badly > need to know! I do not want to get into a flame war here and will not participate in one, but the preceding comment is indicative of the reasons whey experimental structural chemists are often less than enthusiastic about the proliferation of modeling packages and the embarrassing ease with which they can be employed. It is fortunate that the late Linus Pauling didn't have such tools or he might have tried to invoke cis peptide linkages instead of trans and hence would have not found his alpha helix and beta sheet structures. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Dr. William T. Winter Phone: (315)470-6876 315 Baker Lab FAX: (315)470-6856 SUNY-ESF Internet: wtwinter@mailbox.syr.edu Syracuse, NY 13210-2786