>From lybrand@proteus.bioeng.washington.edu Thu May 22 17:50 EDT 1997 Received: from mailhost1.cac.washington.edu for lybrand@proteus.bioeng.washington.edu by bedrock.ccl.net (8.8.3/950822.1) id RAA01446; Thu, 22 May 1997 17:50:35 -0400 (EDT) Received: from proteus.bioeng.washington.edu (proteus.bioeng.washington.edu [128.95.145.1]) by mailhost1.cac.washington.edu (8.8.4+UW96.12/8.8.4+UW97.03) with SMTP id OAA17443 for ; Thu, 22 May 1997 14:50:33 -0700 Received: by proteus.bioeng.washington.edu (940816.SGI.8.6.9/5.6) id OAA19127; Thu, 22 May 1997 14:50:32 -0700 Date: Thu, 22 May 1997 14:50:32 -0700 From: lybrand@proteus.bioeng.washington.edu (Terry P. Lybrand) Message-Id: <199705222150.OAA19127@proteus.bioeng.washington.edu> To: jkl@ccl.net Subject: 98.01.05 Pacific Symposium on Biocomputing ******************************Call for Papers********************************** Molecular modeling in drug design and biotechnology Pacific Symposium on Biocomputing '98 (http://cgl.ucsf.edu/psb) Co-chairs: Terry P. Lybrand, University of Washington, Seattle Teri E. Klein, University of California, San Francisco Jurgen Bajorath, Bristol-Myers Squibb Research Institute and University of Washington, Seattle. The Pacific Symposium on Biocomputing (PSB-98) is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. We are currently soliciting manuscripts for the track/session "Molecular modeling in drug design and biotechnology" and/or abstracts for an accompanying poster session. This session will highlight state-of-the-art molecular modeling approaches which aid in small molecular and structure-based drug design and protein engineering. These include approaches to analyze the energetics and dynamics of macromolecular structures and their interactions with various ligands. Advances in the generation and assessment of molecular models of proteins and protein-ligand complexes will be discussed. One focal point will be new developments and advances in computational tools to perform automated ligand docking to target receptor sites, including the design of new or modified ligands with desired receptor binding properties. New methods and practical examples of computer-aided protein engineering will also be highlighted. Contributions from all areas of pharmaceutical or biological research are encouraged to illustrate the increasing importance of computational methods in drug development. PSB-98 will publish peer-reviewed full papers in an archival proceedings. Manuscripts must adhere to the guidelines set forth on the the PSB web page. Full papers must not have been previously presented or published, nor currently submitted to another journal. Once accepted to the conference, a paper may be submitted for journal publication. Each manuscript will be refereed by at least four reviewers. Authors who do not wish to submit a full paper are welcome to submit a 1-2 page abstract as outlined on the PSB web page, which will be distributed at the meeting separately from the archival proceedings. The deadline for paper submission is July 14, 1997. Abstracts may be submitted until October 1. Papers must be submitted to: PSB-98 c/o Section on Medical Informatics Stanford University Medical School, MSOB X215 Stanford, CA 94305-5479 USA Electronic submission of papers is encouraged. Format requirements for electronic submission will be available on the web page (http://www.cgl.ucsf.edu/psb) or from Russ Altman (altman@smi.stanford.edu). Electronic papers will be submitted directly to Dr. Altman. We prefer that all one page abstracts are submitted electronically. Please send them to us in plain ascii text or as a Microsoft Word file. If this is impossible, please contact Teri Klein (klein@cgl.ucsf.edu). Contact information: Terry Lybrand Univ. of Washington, Box 351750 Phone: (206)-685-1515 (office); (206)-685-1512 (lab) E-mail: lybrand@proteus.bioeng.washington.edu Jurgen Bajorath Bristol-Myers Squibb Res. Inst. bajorath@protos.bms.com Tel (206) 727-3612 Teri Klein UCSF Phone: (415) 476-0663 email: klein@cgl.ucsf.edu For more information on the Pacific Symposium on Biocomputing, please see our web site at http://www.cgl.ucsf.edu/psb. ****************************************************************************** -------------------------------------cut here----------------------------- ----------------------------------------------------------- Terry P. Lybrand, Ph.D. Associate Professor, Molecular Bioengineering Adjunct Associate Professor, Chemistry Director, Whitaker Molecular Modeling Laboratory Center for Bioengineering Univ. of Washington, Box 351750 Seattle, WA 98195-1750 Phone: (206)-685-1515 (office); (206)-685-1512 (lab) Fax: (206)-616-4387 E-mail: lybrand@proteus.bioeng.washington.edu WWW: http://weber.u.washington.edu/~lybrand From tajkhors@mbp-sgi7.inet.dkfz-heidelberg.de Tue May 27 06:45:01 1997 Received: from ns1.DKFZ-Heidelberg.de for tajkhors@mbp-sgi7.inet.dkfz-heidelberg.de by www.ccl.net (8.8.3/950822.1) id GAA07892; Tue, 27 May 1997 06:39:17 -0400 (EDT) Received: from mbp-sgi7.inet.dkfz-heidelberg.de (mbp-sgi7.inet.dkfz-heidelberg.de [193.174.48.96]) by ns1.DKFZ-Heidelberg.de (8.7.3/DKFZ-8.6.4) with ESMTP id MAA20628 for ; Tue, 27 May 1997 12:36:27 +0200 (MET DST) Received: (tajkhors@localhost) by mbp-sgi7.inet.dkfz-heidelberg.de (940816.SGI.8.6.9/DKFZ-8.6.4) id MAA15218 for chemistry@www.ccl.net; Tue, 27 May 1997 12:33:40 +0200 From: "Emadeddin Tajkhorshid" Message-Id: <9705271233.ZM15216@mbp-sgi7.inet.dkfz-heidelberg.de> Date: Tue, 27 May 1997 12:33:38 -0600 Reply-To: E.Tajkhorshid@DKFZ-Heidelberg.de X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net (Computational Chemistry List) Subject: QM MD Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear all I am looking for any info. about quantom chemical molecular dynamics. Any program, web site and .... Thanx -- Emad ********************************************************************* E. Tajkhorshid German Cancer Research Center; DKFZ Tel: +49 6221 42 2339 Dept. Molecular Biophysics (0810) FAX: +49 6221 42 2333 P.O.Box 101949 69009 Heidelberg, FRG Email: E.Tajkhorshid@DKFZ-Heidelberg.de ********************************************************************* * "Never express yourself more clearly than you think." -Niels Bohr * ********************************************************************* From bruno@antas.agraria.uniss.it Tue May 27 09:45:02 1997 Received: from ssmain.uniss.it for bruno@antas.agraria.uniss.it by www.ccl.net (8.8.3/950822.1) id IAA08530; Tue, 27 May 1997 08:58:31 -0400 (EDT) Received: from antas.agraria.uniss.it by ssmain.uniss.it with SMTP (1.39.111.2/16.2) id AA228117758; Tue, 27 May 1997 14:55:58 +0200 Date: Tue, 27 May 1997 14:56:34 +0100 (NFT) From: "Dr. Bruno Manunza" To: E.Tajkhorshid@DKFZ-Heidelberg.de Cc: Computational Chemistry List Subject: Re: CCL:QM MD In-Reply-To: <9705271233.ZM15216@mbp-sgi7.inet.dkfz-heidelberg.de> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 27 May 1997, Emadeddin Tajkhorshid wrote: > Dear all > > I am looking for any info. about quantom chemical molecular dynamics. Any > program, web site and .... > > Thanx > > > -- > Emad Dear Emad, have a look to the links in the software and Molecular Modeling pages on our site at: http://antas.agraria.uniss.it you'll find listed both programs and urls. Hope it helps Regards Bruno Dr Bruno Manunza DISAABA (Dept. of Agricultural Environm. Sci) University of Sassari V.le Italia 39 07100 Sassari, ITALY phone: 39 79 229215 fax: 39 79 229276 e-mail: bruno@antas.agraria.uniss.it e-mail: bruno@tharros.dipchim.uniss.it e-mail: gx6bot81@cray.cineca.it web: http://antas.agraria.uniss.it From qibvigap@lg.ehu.es Tue May 27 09:51:37 1997 Received: from lgsx01.lg.ehu.es for qibvigap@lg.ehu.es by www.ccl.net (8.8.3/950822.1) id JAA08674; Tue, 27 May 1997 09:22:21 -0400 (EDT) Received: from lgdx02.lg.ehu.es by lgsx01.lg.ehu.es (4.1/4.7 ) id AA09957; Tue, 27 May 97 15:20:11 +0100 Received: by lgdx02.lg.ehu.es (5.65/4.7) id AA00419; Tue, 27 May 1997 15:30:33 +0100 Date: Tue, 27 May 1997 15:30:33 +0100 (WET DST) From: Pablo Vitoria Garcia X-Sender: qibvigap@lgdx02 To: ccl Subject: Summary: Coupled Cluster (CCD, CCSD) in G94 Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Thanks to everyone who helped with my question about CC optimisations in G94. All the answers are summarized below, following my message. In a few words: - CCSD optmizations can be done numerically in G94. - Although the convergence criterion can be changed, it seems to a better choice to increment the number of allowed cycles. - CCSD analytical optimizations can be done with ACESS II, which is higly recomended over G94 for CC claculations in general. My question was: > When I tried to optimize a molecule at the CCSD(T) level, I found out > that G94 cannot do that, since there are no analytical gradients > available for that method. Instead I tried CCD, although I guess it's not > so accurate as CCSD. But the wavefunction didn't converge after 50 > iterations. So there go my questions: > > 1. Is there any way (perhaps a non-standard route) to perform an > optimization at the CCSD level with the available numerical gradient? > > 2. The convergence criterion at the beginning of the CCD calculation: > > Iterations= 50 Convergence= 0.100D-07 > > what does it refere to? Can I lower it without affecting too much the > reliability of the calculations? -------------------------------------------------------------------------------- From: "Michael Nolan (WannaBe Quantum Chemist)" You could simply try and increse the number of iterations from 50 the convergence criteria refer simply to the maximum number of iterations(50) and what the difference between two successive iterations (0.100D-07) must be. I don't know too much about G94, our own copy of it still isn't working (even Gaussian Inc. couldn't get it to work!), so I cannot be too specific. -------------------------------------------------------------------------------- From: Qiang Cui If possible, do NOT use Gaussian for CCSD etc. calculations. It's very slow compared to Molpro or ACES. Both of them can handle CCSD(T) very efficiently. However, as far as I know, ACES is the only one that can actually handle CCSD(T) analytical gradient. They have implemented analytical hessian as well for CCSD(T). (and all other approximations as well as excited state extensions.) -------------------------------------------------------------------------------- From: "Eric V. Patterson" G94 can indeed optimize molecules at the CCSD(T) level, just not analytically. This makes the optimization very slow, or course. Frequency calculations become even more painful. You may set the convergence threshold by specifying CCSD(T,conver=N), where N is the desired threshold, 10^-N. I would not be inclined to reduce this figure too far below the default of 8, maybe no lower than 6. You don't mention what starting geometry you are using. It would be advisable to start with a good MP2 of DFT structure. This may help with some of your convergence difficulties. Finally, a personal aside. I use CCSD(T) frequently. It is a very reliable, high-level method. However, I don't use Gaussian for it. The ACES II package from the Quantum Chemistry Program at the University of Florida (http://qtp.ufl.edu/Aces2) is a robust program designed specifically for coupled-cluster applications. Optimizations are done analytically. It is no more difficult to use than Gaussian, and is superior for CC calculations, in my opinion. -------------------------------------------------------------------------------- From: Doug Fox Gaussian 94 can optimize structures with CCSD and CCSD(T) but since only energy calculations are available it will use numerical gradients instead. For CCD there are analytic gradients so the normal optimizer will be used. For numerical gradients the gradient is only as accurate as the energy which is computed. So while you can cut down the convergence with the Conver=N option the possible accuracy of your structure is directly affected. If the convergence is close with 50 cycles you can use the MaxCyc=M option to increase the number of iterations in the CC. For CCD I would highly recommend against reducing these because the optimization assumes that it will get at least the default accuracy in the gradients. -------------------------------------------------------------------------------- From: Hui-Hsu Tsai I think the program "PSI" can do CCSD(T) geometry optimization. -------------------------------------------------------------------------------- From: Jan Hrusak You may have also a look to our recent paper on the comparisons of all the CC based methods (CCD, CCSD, CCSD(T), BD, BD(T), QCISD, QCISD(T)) in J. Chem. Phys. 1997, 106, 7185. In general the Gaussian allows you to do numerical gradient calculations just using the opt command. The number of iterations can be increased by typing the IOP(9/6=xxxx) option. -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Pablo Vitoria Garcia Departamento de Quimica Inorganica, Facultad de Ciencias Universidad del Pais Vasco (UPV/EHU) Apartado 644, E-48080 Bilbao SPAIN e-mail: qibvigap@lgdx02.lg.ehu.es Phone: +34 4 4647700 Ext. 2450 -------------------------------------------------------------------------------- From anina01@iona.cryst.bbk.ac.uk Tue May 27 10:48:23 1997 Received: from iona.cryst.bbk.ac.uk for anina01@iona.cryst.bbk.ac.uk by www.ccl.net (8.8.3/950822.1) id KAA09640; Tue, 27 May 1997 10:30:22 -0400 (EDT) Received: from jura.cryst.bbk.ac.uk by iona.cryst.bbk.ac.uk; (5.65v3.2/2.1/09Sep96-1332PM) with SMTP id <9705271431.AA00843@iona.cryst.bbk.ac.uk>; Tue, 27 May 1997 15:31:09 +0100 Received: from localhost by jura.cryst.bbk.ac.uk (931110.SGI) id AA28994; Tue, 27 May 97 15:31:08 +0100 Date: Tue, 27 May 1997 15:31:07 +0100 (BST) From: Alex Ninaber X-Sender: anina01@jura.cryst.bbk.ac.uk To: ccl Subject: Wanted: simple MD trajectory viewer for reasonable sized systems Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, I am trying to find a free and simple MD trajectory viewer for Linux/xwindows with source. It does not have to be specifically for biomolecular structures, as long if I can view a trajectory of moving dots with bonds. I have tried VMD, and basically I think it is way too slow compared with a single frame viewer as Rasmol (to say it in other words: it can be done much faster). I would be happy with sources of any graphical primitives as well, so I can build the viewer myself. If there is any interest in these kind of programs, I'll maybe put some more effort in it. Alex Ninaber From bianco@lord.Colorado.EDU Tue May 27 13:45:04 1997 Received: from lord.Colorado.EDU for bianco@lord.Colorado.EDU by www.ccl.net (8.8.3/950822.1) id NAA10956; Tue, 27 May 1997 13:16:46 -0400 (EDT) Received: by lord.Colorado.EDU (920330.SGI/911001.SGI) for chemistry@www.ccl.net id AA04277; Tue, 27 May 97 11:14:53 -0600 From: bianco@lord.Colorado.EDU (Roberto Bianco) Message-Id: <9705271714.AA04277@lord.Colorado.EDU> Subject: MCSCF / selection of configurations To: chemistry@www.ccl.net (ccl) Date: Tue, 27 May 1997 11:14:53 -0600 (MDT) X-Mailer: ELM [version 2.4ME+ PL26 (25)] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CCLers, I would like to do a state-averaged MCSCF calculation for the first few electronic states of a relatively large system. Are there references about the possible strategies one could use to select the relevant configurations for my particular case ? I will summarize to the list. Thanx in advance, Roberto -- Roberto Bianco / Department of Chemistry & Biochemistry University of Colorado / Campus Box 215 / Boulder, CO 80309 / USA bianco@lord.colorado.edu / phone +(303) 492-3504 / fax +(303) 492-5894 From aholder@CCTR.UMKC.EDU Tue May 27 13:50:12 1997 Received: from ns3.umkc.edu for aholder@CCTR.UMKC.EDU by www.ccl.net (8.8.3/950822.1) id MAA10751; Tue, 27 May 1997 12:46:36 -0400 (EDT) Received: from holder.chem.umkc.edu by ns3.umkc.edu (5.65v3.2/1.1.10.5/01Jan97-0538PM) id AA11230; Tue, 27 May 1997 11:45:13 -0500 X-Mailer: InterCon tcpCONNECT4 4.0.3 (Macintosh) Mime-Version: 1.0 Message-Id: <9705271145.AA11398@134.193.11.2> Date: Tue, 27 May 1997 11:45:11 -0500 From: "Andy Holder" To: pino@jsbach.dichi.unina.it, chemistry@www.ccl.net Subject: Re: CCL:AM1 frequencies scaling Content-Type: Text/Plain; charset=US-ASCII Content-Disposition: Inline Netters, Guiseppe Milano posed the following question a week or so ago: > I would appreciate to receive information about scaling of AM1 frequencies I though I would reply as the author of two papers in this area: J. Mol. Struct. (THEOCHEM); 1993, 281, 141 (AM1 results) J. Mol. Struct. (THEOCHEM); 1997 in press. (SAM1 results) Unfortunately, things in the semiempirical world are not as simple as in the case of ab initio calculations in this area. The AM1 paper above clearly showed that no single factor would solve the problem of scaling all vibrational types. The errors for the different motions was widely variable, although there were clear trends that were easily explainable by the relative simplicity of the semiempirical orbital descriptions. A quite complex scheme of corrections was proposed in that paper. The SAM1 paper basically says the same thing, although the error analysis has been greatly simplified, making adjustment of the vibrations to experimental results easier. I have listed some selected data below to support this: Errors Vib. Type #Examples SAM1 |SAM1| AM1 |AM1| ----------------------------------------------------------------- All 442 0.7% 9.0% 4.9% 9.6% Str. (non-H) 69 14.0 15.7 14.9 18.2 Str. (C-H) 105 -2.6 3.8 4.4 4.5 Bends 75 -0.8 10.5 6.3 10.4 Rock/Wags 116 0.8 8.3 4.5 8.9 Defs. 66 -2.7 8.0 -1.8 7.8 Tors. 11 -20.4 21.2 -16.2 16.3 The take-home lessons: 1. Only vibrational types that have signed and unsigned errors of the same magnitude will likely benefit from adjustment. 2. SAM1 non-H stretching modes can be scaled by multiplying by 0.86 AM1 non-H stretching modes can be scaled by multiplying by 0.85 3. SAM1 torsional modes can be scales by multiplying by 1.2563 AM1 torsional modes can be scales by multiplying by 1.1933 4. The TYPE of vibration must be identified before scaling. This is best done with vibrational animation graphics software. I obviously used AMPAC for all of these tasks. Regards, Andy Holder -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- UUUU UUU MMM MMKK KKKK CCCC | ANDREW J. HOLDER UU U MM MMK K CC CC | Assoc. Prof. of Comp./Org. Chemistry UU U MMM M MK KK CCC | Dept. of Chemistry UU U M MM MK KK CC CC | University of Missouri-Kansas City UUUUU MMM M MMKK KK CCCC | Kansas City, MO 64110 KK | aholder@cctr.umkc.edu K | (816) 235-2293, FAX (816) 235-5502 -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From rjm@theory.chem.ubc.ca Tue May 27 14:45:05 1997 Received: from mail-relay.ubc.ca for rjm@theory.chem.ubc.ca by www.ccl.net (8.8.3/950822.1) id OAA11980; Tue, 27 May 1997 14:40:55 -0400 (EDT) Received: from seymour.chem.ubc.ca (root@seymour.chem.ubc.ca [137.82.31.13]) by mail-relay.ubc.ca (8.7.6/8.7.3) with SMTP id LAA17275 for ; Tue, 27 May 1997 11:40:48 -0700 (PDT) Received: from seymour.chem.ubc.ca by seymour.chem.ubc.ca (AIX 3.2/UCB 5.64/1.14) id AA16180; Tue, 27 May 1997 11:40:46 -0700 Sender: rjm@theory.chem.ubc.ca Message-Id: <338B2AAD.167E@theory.chem.ubc.ca> Date: Tue, 27 May 1997 11:40:45 -0700 From: Richard Moss Organization: Dept Chemistry, University of British Columbia X-Mailer: Mozilla 3.0 (X11; I; AIX 2) Mime-Version: 1.0 To: ccl Subject: calculating symmetry Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I was wondering if anyone knows of any code that will calculate the symmetry elements of a group of particles. What I want to do is look at the nearest neighbours around a particle and be able to calculate the degree to which those neighbours have a particular symmetry, ie inversion, reflection etc. I want from this to be able to say how well these particles correspond to tetrahedral, icosahedral etc symmetry, by asking things like "how many planes of symmetry are there, and how 'good' a plane of symmetry is each". thanks, Richard From choic@gusun.georgetown.edu Tue May 27 16:45:07 1997 Received: from gusun.georgetown.edu for choic@gusun.georgetown.edu by www.ccl.net (8.8.3/950822.1) id QAA13042; Tue, 27 May 1997 16:34:20 -0400 (EDT) Received: from molmod.georgetown.edu (molmod.chem.georgetown.edu [141.161.23.55]) by gusun.georgetown.edu (8.8.5/8.8.5) with ESMTP id QAA03668 for ; Tue, 27 May 1997 16:33:38 -0400 (EDT) Message-Id: <199705272033.QAA03668@gusun.georgetown.edu> From: "Cheol Ho Choi" To: Subject: dipole-quadrupole polarizability & dipole-magnetic dipole polarizability ? Date: Tue, 27 May 1997 16:34:48 -0400 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1155 MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear CCLers, CADPAC program can calculate the electric dipole-quadrupole polarizability tensor (A), electric dipole-magnetic dipole polarizability tensor (G'), and their derivative w.r.t. nuclear displacement coordinates. It seems that it is possible to evaluate above quantities numerically using G94. Is there anyone who knows how to do this? Thanks, Cheol-Ho Choi Georgetown University From bruno@antas.agraria.uniss.it Tue May 27 17:45:06 1997 Received: from ssmain.uniss.it for bruno@antas.agraria.uniss.it by www.ccl.net (8.8.3/950822.1) id RAA13598; Tue, 27 May 1997 17:19:41 -0400 (EDT) Received: from antas.agraria.uniss.it by ssmain.uniss.it with SMTP (1.39.111.2/16.2) id AA001137974; Tue, 27 May 1997 23:19:34 +0200 Date: Tue, 27 May 1997 23:20:11 +0100 (NFT) From: "Dr. Bruno Manunza" To: Alex Ninaber Cc: ccl Subject: Re: CCL:Wanted: simple MD trajectory viewer for reasonable sized systems In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 27 May 1997, Alex Ninaber wrote: > Hi all, > > I am trying to find a free and simple MD trajectory viewer for > Linux/xwindows with source. It does not have to be specifically > for biomolecular structures, as long if I can view a trajectory > of moving dots with bonds. I have tried VMD, and basically > I think it is way too slow compared with a single frame viewer > as Rasmol (to say it in other words: it can be done much faster). > I would be happy with sources of any graphical primitives > as well, so I can build the viewer myself. If there is any interest in > these kind of programs, I'll maybe put some more effort in it. > > Alex Ninaber Dear Alex, you may check the gOpenMol program at http://laaksonen.csc.fi/gopenmol/gIntro.htmls which support several molecular formats; also Xmol http://www.msc.edu/msc/docs/xmol/XMol.html is suitable for animating sequences of XYZ files. One more animation program is Moviemol http://chem-www.mps.ohio-state.edu/~lars/moviemol.html which works on both PC and UNIX environments. For further infos check our CompChem software page at http://antas.agraria.uniss.it/software.html Bye Bruno Dr Bruno Manunza DISAABA (Dept. of Agricultural Environm. Sci) University of Sassari V.le Italia 39 07100 Sassari, ITALY phone: 39 79 229215 fax: 39 79 229276 e-mail: bruno@antas.agraria.uniss.it e-mail: bruno@tharros.dipchim.uniss.it e-mail: gx6bot81@cray.cineca.it web: http://antas.agraria.uniss.it From yus@dragon.crs.uc.edu Tue May 27 20:45:08 1997 Received: from blues.fd1.uc.edu for yus@dragon.crs.uc.edu by www.ccl.net (8.8.3/950822.1) id TAA14263; Tue, 27 May 1997 19:46:03 -0400 (EDT) Received: from dragon.crs.uc.edu by UCBEH.SAN.UC.EDU (PMDF V5.0-7 #15949) id <01IJDJOFEVWIHMARGS@UCBEH.SAN.UC.EDU> for chemistry@www.ccl.net; Tue, 27 May 1997 19:44:08 -0500 (EST) Received: by dragon.crs.uc.edu (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@www.ccl.net id TAA27079; Tue, 27 May 1997 19:45:16 -0400 Date: Tue, 27 May 1997 19:45:13 -0400 From: Yugal Sharma Subject: getting order parameters from trajectory? To: chemistry@www.ccl.net Reply-to: yus@dragon.crs.uc.edu Message-id: <9705271945.ZM27077@dragon.crs.uc.edu> MIME-version: 1.0 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT I was wondering if anyone knew any way to extract order parameters (S^2) from the trajectory generated by an md simulation (e.g. discover)? I know of fortran programs available to do this, but have not been able to implement them correctly. Any information would be helpful. Thank you. Sincerely, Yugal Sharma -- __________________________________________________________________________ Yugal K. Sharma Lab: (513) 556-9272 Graduate Assistant (513) 556-9277 Department of Chemistry University of Cincinnati Home: (513) 481-6386 Email: yus@dragon.crs.uc.edu yus@pegasus.crs.uc.edu __________________________________________________________________________