From AEMHC@CUNYVM.CUNY.EDU Mon Dec 19 03:22:40 1994 Received: from phem3 for AEMHC@CUNYVM.CUNY.EDU by www.ccl.net (8.6.9/930601.1506) id CAA15152; Mon, 19 Dec 1994 02:53:30 -0500 Received: from CUNYVM.CUNY.EDU (MAILER@CUNYVMV2) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HKT90WU4TC94GJSZ@phem3.acs.ohio-state.edu>; Mon, 19 Dec 1994 02:53:24 EDT Received: from CUNYVM.CUNY.EDU (NJE origin AEMHC@CUNYVM) by CUNYVM.CUNY.EDU (LMail V1.2a/1.8a) with RFC822 id 0838; Mon, 19 Dec 1994 02:52:26 -0500 Date: Mon, 19 Dec 1994 02:39:45 -0500 (EST) From: Artem Masunov Subject: Urea: Flat or Chiral in the Gase Phase? To: chemistry@ccl.net Message-id: <01HKT90WU4TE94GJSZ@phem3.acs.ohio-state.edu> Content-transfer-encoding: 7BIT Dear Netters, Doing my PhD research in Theoretical Chemistry, I found (at PM3 and MP2/G95** levels, but not at AM1 and HF), that urea, (H2N)2C=O, is nonplanar with two conformations (Cs and C2 symmetry), instead of flat C2v, like in crystal. Can anybody adwise me how to get references on experimental (MW or ED) geometry of urea molecules in gase phase? Vibrations and interconversion barriers are also wanted. Somebody told me to ask Prof.B.P.Winnewisser. What is his E-mail address? I'v heard, there is specific database on gase data like CCSDB on crystals. It showld locate somewhere in Germany. Does it have remote access? Alternatively I am interested in new reference books (those old ones I found in the library say nothing about urea). I will be greately appreciated for all responces. Send directly to me (I am not subscriber of CCL) and I'll summarize. Regards, Artem. --------------------------Artem E. Masunov---------------------------- | Chemistry Department, Hunter College, City University of New York | | E-mail: AEMHC@cunyvm.cuny.edu, tel: 212/725-0317, fax:772-5332 | ---------------------------------------------------------------------- From gedeck@pctc.chemie.uni-erlangen.de Mon Dec 19 06:22:53 1994 Received: from faui45.informatik.uni-erlangen.de for gedeck@pctc.chemie.uni-erlangen.de by www.ccl.net (8.6.9/930601.1506) id GAA16889; Mon, 19 Dec 1994 06:18:03 -0500 Received: from faui43.informatik.uni-erlangen.de by uni-erlangen.de with SMTP; id AA05680 (5.65c-6/7.3w-FAU); Mon, 19 Dec 1994 12:17:41 +0100 Received: from pctc.chemie.uni-erlangen.de by immd4.informatik.uni-erlangen.de with SMTP; id AA16055 (5.65c-6/7.3m-FAU); Mon, 19 Dec 1994 12:17:37 +0100 Received: from pc1.chemie.uni-erlangen.de by pctc.chemie.uni-erlangen.de (AIX 3.2/UCB 5.64/4.03) id AA21699; Mon, 19 Dec 1994 12:17:31 +0100 Received: by pc1.chemie.uni-erlangen.de (AIX 3.2/UCB 5.64/4.03) id AA12998; Mon, 19 Dec 1994 12:17:31 +0100 Date: Mon, 19 Dec 1994 12:17:29 +0100 (NFT) From: Peter Gedeck To: chemistry@ccl.net Subject: Scaling of vibrational frequencies Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, this time I would like to ask, why vibrational frequencies are usually scaled by a factor (0.89-0.9)? As far as I know, this is independent of the calculational method used (ab-initio or semiempirical). So, is it a deficiency of the theoretical approach or is it just a question of the accuracy of the calculation? I'm looking forward to hear any comments or pointers to literature dealing with this question. Peter Peter Gedeck Inst. f. Physikalische Chemie I Egerlandstrasse 3 91058 Erlangen Germany Tel: ++9131 - 85 7335 Fax: ++9131 - 85 8307 E-Mail: gedeck@pctc.chemie.uni-erlangen.de WWW: http://pctc.chemie.uni-erlangen.de/~gedeck/gedeck.html From underhil@hp.rmc.ca Mon Dec 19 09:22:48 1994 Received: from sv2.rmc.ca for underhil@hp.rmc.ca by www.ccl.net (8.6.9/930601.1506) id IAA19093; Mon, 19 Dec 1994 08:47:58 -0500 Received: from underhill.rmc.ca by sv2.rmc.ca with SMTP id AA04300 (5.67b/IDA-1.5 for ); Mon, 19 Dec 1994 08:47:28 -0500 Date: Mon, 19 Dec 1994 08:47:28 -0500 Message-Id: <199412191347.AA04300@sv2.rmc.ca> X-Sender: underhil@137.94.5.141 X-Mailer: Windows Eudora Version 1.4.3 Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable To: chemistry@ccl.net From: underhil@hp.rmc.ca (Ross Underhill) Subject: summary: equilibriation of liquids Attached is a list of replies I got to my query about accelerating convergence to equilibrium for a liquid and making sure you are at a global minimum. =20 Part of my original problem was that my liquid was made up of large branched molecules which tend to get hooked on each other. Also I suspect my periodic box was just not big enough. While there were some unique ideas, most of the replies suggested using either monte carlo codes or "annealing" at higher temperatures. I confess I'm not to keen on the latter as I've found it to be a two edged sword. Yes, it helps you get over barriers that geometry minimization can't but at the same time the other side of the barrier can be a high energy configuration which you then get frozen in. Anyway, Thanks a lot to all who replied. Here are the replies except for one which asked not to be passed on. when we simulate the supercritical dilute mixture system close to the critical point, we will find the strange noise (fluctuation) in the monitor values such as temperature, if we prepare the critical state directly. That is, the initial state is the critical state itself. However if I prepare the critical state close to the critical point= gradually using the liquid equilibrium state near triple point, the fluctuations of monitor value are very reasonable. It seems to concern the density fluctuations. If there exists artificial density fluctuations in the system, the fluctuations of monitor values are not real and the state must be a local minimum. furthermore, this phenomena depends on the ensemble. For example, If we use Nose emsemble, we can not avoid the un-natural fluctuations of monitor values. This influences on the time-dependent correlation functions. I think you should use microcanonical ensemble after preparing state using velocity scaling MD. Your idea is very resonable to get the equilibrium state far from triple point. The frequecy of collisions is much greater in the liquid state near triple point than in the state far from the triple point. So the simulation time is shorter and the state we get seems to be a global minimum. I'm not sure what state you need to prepare, because of there seems to be the same problem. You can avoid getting the local minimum state if you use the near-triple-pointstate as an initial state and then gradually prepare the state that you need. For the dilute mixture, this is much more important, because the solvent molecules gather around the solute molecule because of density fluctuations= in solvent. If there exists un-natural density fluctuations in solvent, these influences the radial distribution between solute and solvent, and hence has influence on the solubility. If you need the solubility, grand canonical montecarlo is best. Will you estimate the solubility by integrating the radial distribution function ? Good luck ! = ___________________________________________________________________________= _ ( Masahiko Katagirti Email : v_uk@biosym.com = ) ( CompuServe : 71651.2173@compuserve.com = ) ( Biosym Technologies, INC. Phone : 619-546-5389= ) ( Fax : 619-458-0136= ) ( 9685 Scranton Road, San Diego, CA 92121-3752= ) (___________________________________________________________________________= _) There are some musings on equilibration in the Questions and Net parts of the amber web material, http://www.amber.ucsf.edu/amber/amber.html which may be of interest. Bill Ross I am interested in similar problems of solvation with glucose derivatives. I'm just getting started, but what I have done to avoid the local minimum problem is perform simulated annealing. I start the box of liquid at 1000K, cooling geometrically to 300K. High temperature dynamics should allow the system to sample a good portion of phase space, and hopefullly the minimum conforomation will be a true global minimum. This comes from my days as an NMR spectroscopist, where this is a the technique used. During this annealing with NMR, however, the NOE force constants were scaled high and the other forces were scaled up to their full values as the system cooled. I haven't scaled specific interactions with the current modeling I am doing. As I am just starting out, I'm not sure if this is going to work or not, but it does have some intuitive justification. Good luck, and keep in touch. James Brown Center for Advanced Research in Biotechnology Rockville, MD Heating up the sample to a high temperature (say 700K), running a (short) trajectory and then cooling down (slowly) to the desired temperature should aid equilibration in any NVT ensemble. Cheers, 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 =7F=7F=7F=7F=7F=16=7F=7F=FF=FF=02=16=7F=7Fw=7F=E0 =7F=7F=FF=FF=E2- on CCL, take a look at the following paper: "Methods for Accelerating Chain Folding and Mixing", Liu and Berne, J. Chem. Phy. 99(8), 15 oct. 93. The method discussed there is called "The Fluctuating Sigma Method". They use a time dependent Lennard-Jhones sigma to enhance the mixing of a binary mixture. You can apply this method to your system to get faster equilibration. Best Wishes, Silviu. **************************************************** * Silviu Zilberman * * Tel - Aviv University * * Faculty of Exact Sciences, Chemistry department * * Israel * * * * E-mail: silviu@chemib5.tau.ac.il * **************************************************** Which package are you using? I use insightII running discover 2.95 and have just about overcome most of my teething problems in getting a box of water to behave correctly before using it to model the interactions to various drugs. Discover allows the use of double cutoffs and switching functions to smooth the transitions between the non-bond cutoffs. Kit Lau has a recent paper detailing water simulations in J Phys Chem, 98, No. 35 1994 p8785, although I have not fully read through the paper it does point out some=7F important points about switching functions. If you need further help don't hesitate to ask, though i'll be going home for Christmas and won't be back until early Jan now, i'll give you any help I can. Andy -- ############################################################################= ## Structural and Computation Chemistry Group________chp1aa@uk.ac.surrey -= JANET. Department of= Chemistry___________________________phone_______+44-1483-259591. University of= Surrey______________________________fax_________+44-1483-300803. Guildford,________________________________________ftp___________131.227.110.= 69 Surrey, GU2 5XH, UK_________________WWW = http://www.chem.surrey.ac.uk/~chp1aa/ ############################################################################= ## If you are doing MD on a liquid, it should not get stuck in local minima. A liquid should be diffusing enough that it shouldn't stay long in any one conformation. Have you checked a diffusion constant, or translational order coefficient, or something else to make sure that you are not frozen? I'm not sure why compressing your box would help you converge faster, unless you're pushing molecules into unfavorable contacts, and they squirt out like watermelon seeds. -Steve Stuart steve@chem.columbia.edu This calculation should lead to the interaction of the solute, i, and the solvent, j. This should lead to Gij. But to calculate solubility you also= need to know Gii the energy to release the solute from itself. Are you going to= put i in i solvent to measure this? Butch =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D =E0 =7F=7F=FF=FF=E2- rreira butch@sunlc2.chem.uga.edu Department of Chemistry (706) 542-2050 or 2051 The University of Georgia (706) 542-9454 FAX Athens, GA 30602 Looking for a global minimum energy conformation of bulk water is probably not what you want to do. Generally one looks for establishing a conformational equilibrium at some given temperature and pressure - so that you can obtain the correct distribution of neighbours and orientations of hydrogen bonds, etc. Most of my experience with simulating water has been using MC techniques - many people feel that force-bias MC helps in establishing equilibrium in bulk water simulations. The reference is "On the force bias Monte Carlo simulation of water: methodology, optimization and comparison with molecular dynamics", M. Rao, C. Pangali and B.J. Berne, Mol. Phys. 37, 1773 (1979). My own preference would be to equilibrate your water sample with a MC program, which involves fewer numerical approximations than does MD, and then use the MD when you insert your solute. Heather Gordon Chemistry, Queens' U. What exactly do you mean by "local minima"? How do you detect them? volume to the final value for the full MD run. Is anyone aware of any other tricks one can do to increase the speed of convergence to= equilibrium, or more important avoid falling into a local minimum. I would appreciate any pointers or references I could get. My preferred technique for setting up equilibrium configurations is not to start from a lattice (as most people seem to do) but start with a simulation box much bigger than what I finally want (let's say five times bigger) into which I place the molecules at random positions and with random orientations. Then I start the dynamics and continously make the box smaller, until the correct size is reached. I have never had any problems with that approach, even when generating extremely dense hard-sphere configurations (close to the glass transition). ----------------------------------------------------------------------------= --- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de Chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. A | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ----------------------------------------------------------------------------= --- Dr. Ross Underhill Royal Military College of Canada Kingston, Ontario (613) 541-6000 X6175 From R29CLOSE@ETSU.EAST-TENN-ST.EDU Mon Dec 19 10:22:51 1994 Received: from phem3 for R29CLOSE@ETSU.EAST-TENN-ST.EDU by www.ccl.net (8.6.9/930601.1506) id JAA19890; Mon, 19 Dec 1994 09:55:34 -0500 Received: from ETSU.EAST-TENN-ST.EDU (MAILER@ETSU) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HKTNR6989S94GO7O@phem3.acs.ohio-state.edu>; Mon, 19 Dec 1994 09:55:27 EDT Received: from ETSU.EAST-TENN-ST.EDU (NJE origin R29CLOSE@ETSU) by ETSU.EAST-TENN-ST.EDU (LMail V1.2a/1.8a) with BSMTP id 1950; Mon, 19 Dec 1994 09:45:53 -0500 Date: Mon, 19 Dec 1994 09:38:55 -0500 (EST) From: David Close Subject: Pentium Replacement?? To: chemistry@ccl.net Message-id: <01HKTNR6989U94GO7O@phem3.acs.ohio-state.edu> Organization: East Tennessee State University Content-transfer-encoding: 7BIT Dear CCL Netters: The Sunday Times contained a story on Intel's Corporate image in light of the Pentium problem. The story said there would not be a general recall of all Pentium's. But rather that Intel had posted information on the INTERNET concerning replacements. Essentially the idea is that a person having problems must call Intel, and they will decide if your problems warrent a replacement. Does anyone have further information? I don't have the phone number and I don't know the INTERNET address to obtain this information. Furthermore, has anyone tried to call Intel and therefore perhaps know what type of information Intel is seeking. Regards, Dave Close From young@slater.cem.msu.edu Mon Dec 19 10:27:05 1994 Received: from slater.cem.msu.edu for young@slater.cem.msu.edu by www.ccl.net (8.6.9/930601.1506) id JAA19565; Mon, 19 Dec 1994 09:30:53 -0500 Received: by slater.cem.msu.edu (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA15655; Mon, 19 Dec 94 09:31:39 -0500 Date: Mon, 19 Dec 94 09:31:39 -0500 From: young@slater.cem.msu.edu (Dave Young) Message-Id: <9412191431.AA15655@slater.cem.msu.edu> To: chemistry@ccl.net Subject: frequency errors Hi, There was a question about why vibrational freqencies are scaled by a factor of about 0.9 irregardless of method. The answer is that all of these frequencies are being computed with a harmonic oscilator approximation. For high frequency modes, the difference between the harmonic oscilator prediction and the exact or Morse potential like behavior is about 10% . If you try to look at very low frequency modes, below a few hundred wave numbers, you will see that the frequencies calculated are off by a large amount. Dave Young young@slater.cem.msu.edu youngdc@msucem -------------------------------------------------------------------------- It can be easily shown that certain methods are not applicable to solving the many particle Schrodinger equation. However, it has not been shown that it is impossible to find an analytic solution. The only question remaining is "Who will have the honor?" -------------------------------------------------------------------------- From pueyo@pinon.ccu.uniovi.es Mon Dec 19 11:24:06 1994 Received: from opalo for pueyo@pinon.ccu.uniovi.es by www.ccl.net (8.6.9/930601.1506) id KAA21040; Mon, 19 Dec 1994 10:49:04 -0500 Received: from pinon.ccu.uniovi.es by etsiig.uniovi.es (PMDF V4.3-10 #4541) id <01HKU284G1S08WWCSL@etsiig.uniovi.es>; Mon, 19 Dec 1994 16:49:13 +0100 (GMT) Received: by pinon.ccu.uniovi.es (1.37.109.10G/16.2) id AA148721998; Mon, 19 Dec 1994 16:46:38 +0100 Date: Mon, 19 Dec 1994 16:46:38 +0100 From: Lorenzo Pueyo Subject: Re: CCL:Cell information on Fe2O3 To: chemistry-request@ccl.net, chemistry@ccl.net Message-id: <01HKU284MN4I8WWCSL@etsiig.uniovi.es> Content-transfer-encoding: 7BIT C. Qian (usdccz73@ibmmail.com) asked: >Does any one have the information about the cell size, positions of atoms, >and space group information of Fe2O3 crystal? Fe2O3 can be found in many different phases. At normal pressure and temperature the thermodinamically most stable phase appears to be $\alpha$-Fe3O3, Hematite, that is isostructural to $\alpha$-Al2O3 or corundum. Crystallographic information for hematite follows: Hexagonal R -3 c (No. 167) Z=6 a=5.0356(1) c=13.7489(7) c/a=7.7303 (ideal hcp = 2.828) Fe at (12c) : (0,0,z) O at (18e) : (x,0,1/4) I could not find x and z values for Fe2O3, but they should be similar to the parameters of corundum: z(Al)=0.352, and x(O)=0.306. Further information on hematite could be found on the next reference: Nat. Bur. Stand. (US) Monogr. 25 (1981) 18-37. Hope this helps you. Best regards, Victor Lua~na +--------------------------------------------+ +---^---/ / ! Victor Lua~na ! | ~ / Just in case ! Departamento de Quimica Fisica y Analitica ! | | you don't ! Universidad de Oviedo, 33006-Oviedo, Spain ! < / remember ! e-mail: victor@hobbit.quimica.uniovi.es ! | / where Oviedo ! phone: (34)-8-5103523 ! |____ ___/ is ;-) ! fax: (34)-8-5103480 ! \/ +--------------------------------------------+ From clecio@iqm.unicamp.br Mon Dec 19 14:22:53 1994 Received: from styx.iqm.unicamp.br for clecio@iqm.unicamp.br by www.ccl.net (8.6.9/930601.1506) id NAA24407; Mon, 19 Dec 1994 13:44:34 -0500 Received: (clecio@localhost) by styx.iqm.unicamp.br (8.6.8/iqm-ansp-1.4) id QAA05232; Mon, 19 Dec 1994 16:43:37 -0200 From: Clecio Fernando Klitzke Message-Id: <199412191843.QAA05232@styx.iqm.unicamp.br> Subject: chemecol list To: chemistry@ccl.net Date: Mon, 19 Dec 1994 16:43:36 -0200 (EDT) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 544 **************************************** *ANNOUNCEMENT OF A NEW DISCUSSION LIST * **************************************** To attend people interested in CHEMICAL ECOLOGY, we created CHEMECOL, a discussion list in this area. To subscribe this list send a mail to listserv@iqm.unicamp.br with the message: subscribe chemecol your name After this any mail to CHEMECOL list should be sended to chemecol@iqm.unicamp.br Thanks, Clecio Fernando Klitzke chemecol list owner clecio@iqm.unicamp.br From underhil@hp.rmc.ca Mon Dec 19 15:23:12 1994 Received: from sv2.rmc.ca for underhil@hp.rmc.ca by www.ccl.net (8.6.9/930601.1506) id OAA24930; Mon, 19 Dec 1994 14:23:06 -0500 Received: from underhill.rmc.ca by sv2.rmc.ca with SMTP id AA07016 (5.67b/IDA-1.5 for ); Mon, 19 Dec 1994 14:22:44 -0500 Date: Mon, 19 Dec 1994 14:22:44 -0500 Message-Id: <199412191922.AA07016@sv2.rmc.ca> X-Sender: underhil@137.94.5.141 X-Mailer: Windows Eudora Version 1.4.3 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: underhil@hp.rmc.ca (Ross Underhill) Subject: Monte Carlo Code Does anyone know where one can get a Monte Carlo version of standard molecular mechanics methods such as Amber, or one of the MM series? Thanks in advance Dr. Ross Underhill Royal Military College of Canada Kingston, Ontario (613) 541-6000 X6175 From brianh@scg.scg.fujitsu.com Mon Dec 19 15:36:05 1994 Received: from mail.barrnet.net for brianh@scg.scg.fujitsu.com by www.ccl.net (8.6.9/930601.1506) id OAA25419; Mon, 19 Dec 1994 14:51:39 -0500 Received: from fujitsu1.fujitsu.com by mail.barrnet.net (8.6.8/BARRNET-8.6.6) id LAA06146; Mon, 19 Dec 1994 11:51:34 -0800 Received: from scg.scg.fai.com (scg.scg.fujitsu.com) by fujitsu1.fujitsu.com (4.1/SMI-4.1) id AA12795; Mon, 19 Dec 94 11:51:55 PST Received: by scg.scg.fai.com (4.1/SMI-4.1) id AA06402; Mon, 19 Dec 94 11:51:57 PST Date: Mon, 19 Dec 94 11:51:57 PST From: brianh@scg.scg.fujitsu.com (Brian Hammond) Message-Id: <9412191951.AA06402@scg.scg.fai.com> To: chemistry@ccl.net Subject: Anharmonic bondlength corrections Dear CCLers, I am computing the potential energy curve for a very floppy diatomic. Even at the most extreme level of theory (MP5 with gigantic basis set) my bond length is too short. I suspect this is due to the difference between the experiment measuring the average bond length not the bottom of the potential. Question: Does anyone know a simple way to get the anharmonic correction between these two distances? I have looked at the Morse potential, but have only found expressions for the energy levels, and no indication whether the Morse potential can treat this problem. Thank you for your help, Brian Hammond ======================================================================== Brian L. Hammond _/_/_/_/ _/_/_/ _/_/_/_/_/ Computational Research Div. _/ _/ _/ _/ Fujitsu America, Inc. _/_/_/ _/_/_/_/_/ _/ 3055 Orchard Drive _/ _/ _/ _/ San Jose, CA 95134 _/ _/ _/ _/_/_/_/_/ Tel: (408) 456-7322 Email: brianh@fai.com From gilson@indigo12.carb.nist.gov Mon Dec 19 17:22:50 1994 Received: from ENH.NIST.GOV for gilson@indigo12.carb.nist.gov by www.ccl.net (8.6.9/930601.1506) id QAA27829; Mon, 19 Dec 1994 16:51:16 -0500 Received: from indigo12.carb.nist.gov by ENH.NIST.GOV (PMDF V4.2-13 #4653) id <01HKU28GL4MO0032TV@ENH.NIST.GOV>; Mon, 19 Dec 1994 16:49:28 EDT Received: by indigo12.carb.nist.gov (931110.SGI/930416.SGI) for @enh.nist.gov:chemistry@ccl.net id AA04348; Mon, 19 Dec 94 16:50:41 -0500 Date: Mon, 19 Dec 1994 16:50:41 -0500 From: gilson@indigo12.carb.nist.gov (Dr. Michael K. Gilson) Subject: molecular display program To: chemistry@ccl.net Message-id: <9412192150.AA04348@indigo12.carb.nist.gov> Content-transfer-encoding: 7BIT Hi, Is there a public-domain molecular display program which can be made to repetitively read and re-read a pdb file? The idea is to have an MD program dump conformations into the file every n steps, and have the display pick these up and display them for a near-real-time display of the trajectory. Thanks, Mike Gilson From elewars@alchemy.chem.utoronto.ca Mon Dec 19 17:29:38 1994 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.6.9/930601.1506) id RAA27955; Mon, 19 Dec 1994 17:05:57 -0500 Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.6.9/8.6.9) id RAA14603 for chemistry@ccl.net; Mon, 19 Dec 1994 17:05:28 -0500 Date: Mon, 19 Dec 1994 17:05:28 -0500 From: "E. Lewars" Message-Id: <199412192205.RAA14603@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: WHY CORRECTIONS TO CALC FREQS Peter Gedeck asked why calc frqs are in error and so must be scaled. The general belief seems to be that it's because the calculations (which use the eigenvalues of a force constant matrix) assume the vibrations are harmonic. However, it has been claimed that "this straightfoward looking consideration is wrong..."; see M. Flock and M. Ramek, Int J. Quantum Chem., Quantum Chem. Symposium 27, 331-341 (1993). Some other refs to vib freq scaling are Possible sources of error in empirical scaling... C. L. Janssen and H. F. Schaefer, J Chem Phys 1991 95 5128. MP2 scaling D. J. DeFrees, J Comp Chem 1985 82 333. There is also a recent (ca. 1993) paper by Pople et al in Israel J Chem on scaling MP2 freqs. === From tony@schroeder.newcastle.edu.au Mon Dec 19 19:22:53 1994 Received: from schroeder.newcastle.edu.au for tony@schroeder.newcastle.edu.au by www.ccl.net (8.6.9/930601.1506) id SAA29083; Mon, 19 Dec 1994 18:58:19 -0500 Received: by schroeder.newcastle.edu.au (AIX 3.2/UCB 5.64/4.03) id AA15797; Tue, 20 Dec 1994 10:57:17 +1000 Date: Tue, 20 Dec 1994 10:57:16 +1000 (EET) From: Tony Dyson To: Computational Chemistry List Subject: Re: CCL:molecular display program In-Reply-To: <9412192150.AA04348@indigo12.carb.nist.gov> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 19 Dec 1994, Dr. Michael K. Gilson wrote: > > Hi, > > Is there a public-domain molecular display program which can > be made to repetitively read and re-read a pdb file? You can always use xmol to animate the entire trajectory when the run is complete. > The idea is to have an MD program dump conformations > into the file every n steps, and have the display > pick these up and display them for a near-real-time > display of the trajectory. > Near-real-time? Can I have an account on your machine?! :-) Tony ================================================================ Mr. Anthony J. Dyson tony@schroeder.newcastle.edu.au Dept. of Physics phone: +49 21 5425 University of Newcastle fax: +49 21 6907 Callaghan, Australia, 2308 ================================================================ From bartberg@qtp.ufl.edu Mon Dec 19 22:22:57 1994 Received: from crunch for bartberg@qtp.ufl.edu by www.ccl.net (8.6.9/930601.1506) id VAA01179; Mon, 19 Dec 1994 21:59:12 -0500 Received: by crunch (5.x/4.11) id AA05771; Mon, 19 Dec 1994 21:59:06 -0500 Date: Mon, 19 Dec 1994 21:59:06 -0500 From: "Micheal Bartberger" Message-Id: <9412200259.AA05771@crunch> To: chemistry@ccl.net Subject: AO coefficients / spin densities in G92 Hello all..... I have a question regarding the calculation of AO coefficients (eigenvectors) for both closed-shell and radical species in G92. My question stems from the fact that, in a semiempirical program such as MOPAC, the eigenvectors are those obtained from a Huckel-type approximation using the valence electrons. For example, the 2p(z) coefficients resulting from an AM1 calculation on ethylene have (for the HOMO) a value of .707 (the old "square root of two over two".) Similarly, the SOMO of the allyl radical will have .707 at one of the CH2 termini and -.707 at the other. My question, then, is this: how, when using typical ab initio basis sets, does one come up with an analagous set of AO coefficients? Since basis sets are comprised of more than one set of basis functions, it seems as though each has its own "coefficient". How does one (if at all) transform this into some sort of "total" coefficient for a given AO at a given eigenvalue at a given atom? (Whew. :) ) I hope this isn't too off the wall...... any references, advice, would be appreciated. The reason for asking is because I am interested in trying to correlate the regioselectivity / stereoselectivity of radical reactions with AO coefficients (this seems easier when using semi- empirical programs) and with spin densities (which leads me to my next question....... On p. 156 and p. 175 of the Gaussian92 users manual, (which shows some sample output of sample calculations), there is a section in the output labeled ATOMIC SPIN DENSITIES is given. How are these values then transformed into a "total spin density" for each atom, which could be correlated with a radical's regioselectivity, and which could be transformed / compared to hyperfine couplings in ESR. Again, any references, pointers, scathing criticisms ;^) are welcome. (If it isn't blatantly obvious, I'm a little new at this..... :) ) I will summarize if there is sufficient interest. Thanks again! Regards, Michael D. Bartberger Department of Chemistry University of Florida bartberg@qtp.ufl.edu bartberg@chem.ufl.edu