From yubofan@guomai.sh.cn Fri May 1 00:28:04 1998 Received: from guomai.sh.cn for yubofan@guomai.sh.cn by www.ccl.net (8.8.3/950822.1) id XAA24336; Thu, 30 Apr 1998 23:42:11 -0400 (EDT) Received: from guomai.sh.cn (email-35 [210.0.0.35]) by guomai.sh.cn (8.8.8/8.8.8) with ESMTP id IAA20092 for ; Fri, 1 May 1998 08:58:43 +0900 (CDT) Message-ID: <35491E70.9A376BC5@guomai.sh.cn> Date: Fri, 01 May 1998 08:59:29 +0800 From: Yubo Fan Reply-To: yubofan@guomai.sh.cn Organization: Department of Chemistry, Fudan University X-Mailer: Mozilla 4.04 [en] (Win95; I) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: Is it possible to display ferrocene by PDB file? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I have optimized the geometry of ferrocene by G94W and the Cartesian coordinates of every atoms was given. Is it possible to use these datas to write a PDB file of ferrocene manually? I think ferrocene is organometallic compound with PI-d type bonds and it is quite different with common organic molecules. Please give me some help. Below is the Cartesian coordinates given by G94W. ---------------------------------------------------------- Center Atomic Coordinates (Angstroms) Number Number X Y Z ---------------------------------------------------------- 1 6 .000000 1.226602 1.737849 2 6 -1.166568 .379041 1.737849 3 6 -.720979 -.992342 1.737849 4 6 .720979 -.992342 1.737849 5 6 1.166568 .379041 1.737849 6 1 .000000 2.307452 1.730160 7 1 -2.194517 .713042 1.730160 8 1 -1.356286 -1.866768 1.730160 9 1 1.356286 -1.866768 1.730160 10 1 2.194517 .713042 1.730160 11 26 .000000 .000000 .000000 12 6 .000000 -1.226602 -1.737849 13 6 1.166568 -.379041 -1.737849 14 6 .720979 .992342 -1.737849 15 6 -.720979 .992342 -1.737849 16 6 -1.166568 -.379041 -1.737849 17 1 .000000 -2.307452 -1.730160 18 1 2.194517 -.713042 -1.730160 19 1 1.356286 1.866768 -1.730160 20 1 -1.356286 1.866768 -1.730160 21 1 -2.194517 -.713042 -1.730160 ---------------------------------------------------------- With best regards Y. Fan -- ============================================================= Yubo Fan Email: yubofan@guomai.sh.cn Organic Synthesis Lab yubofan@fudan.edu.cn The Department of Chemistry Fudan University Phone: 8621-65648139 No. 220 Handan Road Fax: 8621-65641740 Shanghai, 200433 P. R. China ============================================================= From Gabriel.Balint-Kurti@bristol.ac.uk Sat May 2 16:28:25 1998 Received: from dirc.bris.ac.uk for Gabriel.Balint-Kurti@bristol.ac.uk by www.ccl.net (8.8.3/950822.1) id PAA02162; Sat, 2 May 1998 15:33:34 -0400 (EDT) Received: from snow-white.chm.bris.ac.uk by dirc.bris.ac.uk with SMTP-PRIV (PP) with ESMTP; Sat, 2 May 1998 20:33:28 +0100 Received: from pc47.chm.bris.ac.uk (pc47.chm.bris.ac.uk [137.222.40.47]) by snow-white.chm.bris.ac.uk (8.8.7/8.8.6) with SMTP id UAA16164 for ; Sat, 2 May 1998 20:34:13 +0100 (BST) From: Gabriel Balint-Kurti Sender: Gabriel.Balint-Kurti@bristol.ac.uk Reply-To: Gabriel.Balint-Kurti@bristol.ac.uk To: Computational Chemistry List Subject: MOLEC Conference - Registration Deadline Message-ID: Date: Sat, 2 May 1998 20:39:24 +0100 (BST) Priority: NORMAL X-Mailer: Simeon for Win32 Version 4.1.2 Build (32) X-Authentication: none MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Transfer-Encoding: QUOTED-PRINTABLE MOLEC XII European Conference on Dynamics of Molecular Collisions University of Bristol 6-11 September 1998 Bristol, UK=20 Deadline for registration 1 June The registration form and programme for the conference are=20 appended below. =20 Keynote Speakers: Y.T. Lee and J.C. Polanyi The form and programme are also available from the conference=20 Web site: =09http://www.tlchm.bris.ac.uk/molec/molec.htm Also appended announcement of commemoration meeting for=20 Professor Roger Grice to be held Monday 14 September. _________________________________________________________________ MOLEC XII European Conference on Dynamics of Molecular Collisions University of Bristol 6-11 September 1998 Bristol, UK=20 REGISTRATION FORM This form and further information is available from the conference Web site= : =09http://www.tlchm.bris.ac.uk/molec/molec.htm Dates: Registration Forms should be returned with payment by 1st June 1998. Abstracts (1 page of size A4) should be sent in before 15 July 1998. Personal details: Title: __Prof. __Dr. __Mr.__Mrs.__Ms.__Miss (tick preferred salutation) Family/Last Name ____________________________________________________ First Name___________________________________________________________ Institution____________________________________________________________ Address______________________________________________________________ _____________________________________________________________________ _____________________________________________________________________ City__________________________________________________________________ State/Province__________________________________________________________ Country_______________________________________________________________ Mail Code__________________________________ Phone_____________________________________ Fax_______________________________________ Email___________________________________________________ Accompanying Persons (These are people not participating in the conference= =20 but who will accompany the participant): I will be accompanied by the following people: Accommodation for participants with accompanying persons (for participants= =20 without accompanying persons single bedroom accommodation in University=20 residences will be arranged): Please book a total of ______ Single Rooms ______ Double Rooms Special Requirements: Please state any dietary or other special requirements you may have.=20 Posters/Abstracts: A book of abstracts will be published. All participants are encouraged to= =20 submit a 1 page (size A4) abstract. Deadline for submission of the=20 abstract is 15 July. A number of abstracts will be selected for 20=20 minute oral presentations. All participants are encouraged to give poster= =20 presentations of their work. Do you wish your abstract to be considered for an oral presentation?...Yes/= No Do you wish to present a poster?.......................................Yes/= No Payment: The Conference package covers food and accommodation from Sunday evening=20 (6 September) to Friday midday (11 September). Registration and Payment Deadline is 1st June 1998. The cost of the=20 conference package if paid before 1st June 1998 is =A3425. Cheques should be made payable to "University of Bristol". Payment is to be made in pound sterling using a cheque or money order drawn= =20 on a U.K. Bank. Payment should not be sent in other currencies or in such= =20 a form as will result in extra bank charges to the conference. The charge for each accompanying person will be =A3275. This will cover food and accommodation and will include the excursion to=20 Bath and the conference banquet. Late Registration: The deadline for registration is 1st June 1998. Registration after=20 this date will be accepted only if space is available. The cost of the conference package after 1st June 1998 will be =A3475. =20 No exceptions will be made to these charges. Car Parking: The Conference venue is in the middle of Bristol. =20 Car parking space is very limited. ___________________________________________________________________________ Please return the completed registration form, together with payment=20 in pound Sterling, to: Dr. G.G. Balint-Kurti/ MOLEC Conference School of Chemistry University of Bristol Bristol BS8 1TS U.K. Further Information: Further information may be obtained from the conference Web site:=20 (http://www.tlchm.bris.ac.uk/molec/molec.htm) or by writing to Dr. G.G. Balint-Kurti at the above address. Other contact points are: Tel: +44 117 9288313 or +44 117 9287662 Fax: +44 117 9250612 email: MOLEC-98@Bristol.ac.uk =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=3D=3D=3D=3D=3D=3D=3D= =3D=3D MOLEC XII =20 European Conference on Dynamics of Molecular Collisions =20 University of Bristol 6-11 September 1998 Bristol, UK=20 Programme =20 Keynote Speakers: Y.T. Lee; Taipei, Taiwan "Reaction and Dissociation Dynamics using Molecular Beams and 157nm Photons" J.C. Polanyi; Toronto, Canada "Photoinduced charge transfer in complexes and at surfaces"=20 Invited Speakers: A. Aguilar ; Barcelona, Spain =09"Accurate quantum studies of triatomic reactions exhibiting=20 =09relevant quantum effects"=20 J.A. Beswick ; Toulouse, France =09"Photodissociation and caging of molecules embedded in rare=20 =09gas clusters and cryogenic matrices." G.D. Billing ; Copenhagen, Denmark =09"Application of the classical path theory in inelastic and=20 =09reactive scattering." M. Brouard ; Oxford, U.K. =09"Stereodynamical studies of hot atom reactions" R.J. Buenker; Wuppertal, Germany =09"Ab initio potential energy surfaces for chemical reactions" P. Casavecchia ; Perugia, Italy =09"Molecular Beam Studies of Elementary Chemical Reactions"=20 D. Dowek ; Orsay, France =09"Dissociative Charge Transfer and dissociative photoionization=20 =09processes induced in ion/photon-molecule interactions" J.H.D. Eland ; Oxford, U.K. =09"Ionisation to inner valence states of small molecules, and=20 =09its consequences" K.H. Gericke ; Braunschweig, Germany =09"Three Body Processes" D. Gerlich; Chemnitz, Germany =09"Molecular collisions in an ion trap"=20 F.A. Gianturco ; Rome, Italy =09"Ion-molecule scattering" S.K. Gray ; Argonne, U.S.A. =09"Reactive quantum scattering with real wave packets ---=20 =09application to O(1D) + H2 --> OH + H in three dimensions" Z. Herman ; Prague, Czech Republic =09"Dynamics of reactions of doubly-charged ions" C. Jouvet ; Orsay, France =09"Solvation dynamic in small molecular clusters" A. Kowalski; Gdansk, Poland =09"Molecular beam studies of chemiluminescence at thermal=20 =09and hyperthermal energies" G.J. Kroes ; Leiden, The Netherlands =09"Six-Dimensional quantum Dynamics of Dissociative Chemisorption=20 =09of H2 on Cu(100)"=20 H.J. Loesch ; Bielefeld, Germany =09"Steric effects and vector correlations in reactive scattering=20 =09with brute force oriented molecules." R. Naaman ; Weizmann Institute, Israel =09"Relation between structure and reactivity of van der Waals=20 =09complexes"=20 A.J. Orr-Ewing ; Bristol, U.K. =09"State selected chemical reactions"=20 D.H. Parker ; Nijmegen, The Netherlands =09"Velocity Map Imaging" L. Yu. Rusin; Russian Academy of Sciences, Moscow, Russia =09"Dynamics of Collision-Induced Dissociation in four-atomic=20 =09systems" G.C. Schatz ; North Western University, U.S.A. =09"Nonadiabatic Reaction Dynamics"=20 M. Shapiro ; Weizmann Institute, Israel =09"Radiative Recombination and Catalysis Induced by a Sequence=20 =09of Laser Pulses" J.P. Toennies ; Max-Planck-Institut f=FCr Str=F6mungsforschung, G=F6ttingen= , Germany =09"Diffraction and filtering of clusters" W.J. van der Zande ; FOM Institute, The Netherlands =09"New Laboratory Diagnostic Tools for Dissociative Recombination and=20 =09Photodissociation Processes"=20 A number of additional speakers will be selected to present=20 shorter presentations on the basis of submitted abstracts. ***************************************************************************= ***** University of Manchester Department of Chemistry Professor Roger Grice (1941 - 1998) A meeting will be held on the afternoon of Monday 14th September 1998 in th= e=20 Chemistry Department, Manchester University. This meeting will include=20 recollections and scientific contributions related to Roger's work and prov= ide=20 the opportunity for Roger's former students, colleagues, collaborators and= =20 friends to commemorate his scientific achievements and remember his life. The meeting will be preceded by a buffet lunch and will be attended by memb= ers=20 of the family. It is also planned to launch an appeal to establish a prize= or=20 scholarship in Roger's memory at this time. If you wish further details of the meeting, please contact Dr J C Whitehead, Chemistry Department, Manchester University, Manchester M13 9PL. (Tel: 0161-275 4692; Fax: 0161- 275 4598;=20 e-mail: j.c.whitehead@man.ac.uk) Sponsored by the Molecular Beams and Dynamics Group of the Royal Society of= =20 Chemistry. From rrovito@dorian.pch.univie.ac.at Mon May 4 06:28:45 1998 Received: from mailbox.univie.ac.at for rrovito@dorian.pch.univie.ac.at by www.ccl.net (8.8.3/950822.1) id GAA08254; Mon, 4 May 1998 06:16:01 -0400 (EDT) Received: from dorian.pch.univie.ac.at (dorian.pch.univie.ac.at [131.130.194.72]) by mailbox.univie.ac.at (8.8.4/8.8.4) with SMTP id MAA32158 for ; Mon, 4 May 1998 12:15:53 +0200 Received: by dorian.pch.univie.ac.at (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA08002; Mon, 4 May 98 12:15:04 +0200 From: "Renato Rovito" Message-Id: <9805041215.ZM8000@dorian.pch.univie.ac.at> Date: Mon, 4 May 1998 12:15:04 +0000 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@www.ccl.net Subject: Lipid Membrane Model Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Dear CCL, I'm a student of the University of Vienna, recently I was Involved in lipid simulation research. In particular, I'd like to perform potential procedures for computer graphic modelig of phospholipid-ligand interaction consistent with the results of experimental NMR binding studies. The my actual problem is to find a good Lipid Membrane Model for my computer modeling studies, I seen that there are a lot of works on this topic, but I still have not found a place in which is possible to get one model. Could you help me with this Sincerely Renato Rovito From dimitris@boris.3dp.com Mon May 4 10:28:46 1998 Received: from worf.ndepot.com for dimitris@boris.3dp.com by www.ccl.net (8.8.3/950822.1) id KAA09600; Mon, 4 May 1998 10:27:19 -0400 (EDT) Received: from boris.3dp.com ([199.33.182.1]) by worf.ndepot.com (8.7.6/8.7.3) with SMTP id IAA26006 for <@worf.ndepot.com:CHEMISTRY@www.ccl.net>; Mon, 4 May 1998 08:34:39 -0400 Received: from telesis.3dp.com (telesis.3dp.com [199.33.182.78]) by boris.3dp.com (951211.SGI.8.6.12.PATCH1502/950213.SGI.AUTOCF) via SMTP id KAA23184 for ; Mon, 4 May 1998 10:29:43 -0400 Received: by telesis.3dp.com with Microsoft Mail id <01BD7747.50ED1520@telesis.3dp.com>; Mon, 4 May 1998 10:28:02 -0400 Message-ID: <01BD7747.50ED1520@telesis.3dp.com> From: "Dimitris K. Agrfiotis" To: "'CHEMISTRY@www.ccl.net'" Subject: Knotted molecules? Date: Mon, 4 May 1998 10:28:01 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Are there any known cases of knotted molecules? Single molecules contining knots, that is, not chained molecules (concatenanes). Thanks, ___ Dimitris K. Agrafiotis, PhD | E-mail: dimitris@3dp.com 3-Dimensional Pharmaceuticals, Inc. | Tel: (610) 458-6045 665 Stockton Drive, Suite 104 | Fax: (610) 458-8249 Exton, PA 19341 From heacm@jazz.ucc.uno.edu Mon May 4 13:29:03 1998 Received: from jazz.ucc.uno.edu for heacm@jazz.ucc.uno.edu by www.ccl.net (8.8.3/950822.1) id MAA10442; Mon, 4 May 1998 12:55:11 -0400 (EDT) Received: from slater (slater.chem.uno.edu) by jazz.ucc.uno.edu (PMDF V5.0-4 #11893) id <01IWMUYEURQ88XD0HC@jazz.ucc.uno.edu>; Mon, 04 May 1998 11:54:39 -0600 (CST) Date: Mon, 04 May 1998 11:51:21 -0500 From: Howard Alper Subject: Re: Simulation of metals Sender: heacm@jazz.ucc.uno.edu To: CHEMISTRY@www.ccl.net Cc: heacm@jazz.ucc.uno.edu Message-id: <354DF209.446B@jazz.ucc.uno.edu> Organization: University of New Orleans MIME-version: 1.0 X-Mailer: Mozilla 3.0 (X11; U; AIX 1) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit Hello all, Some time back I asked the list for information on the simulation of metals using CHARMM or DISCOVER. Below is a summary of the responses. I apologize for the delay. A belated thanks to all who answered my query. Sincerely, Howard Alper _____________________________________________________________________ Dear Dr. Alper I have done and seen several papers on metal surface simulations (most of the metals).I used the De Pristo's CEM potential. I have seen people using EAM. I guess the codes are available from the authors free of cost for academic use. They have their own MD codes, so I am afraid they cannot be easily integrated with CHARMM or DISCOVER. But, De Pristo's code is pretty easy to follow and can be modied very easily. Sincerely Vijaya Kumar _____________________________________________________________________ Dear Dr. Alper I dont have de Pristo's email address but I know he is with Iowa State University's Chemistry department. You can contact Prof. Barbara Garrison at P ennState Univ. She also used his code and her email address is bjg@galilei.chem.psu.edu You can just do a literature search on De Pristo or Garrison. There will bemany actually tons of papers on metal simulations. I have just published one paper on such stuff in JCP in 1997. I used CEM potential to simulate Cu 100 surface. I used smart MCrather than MD. For my own entertainment, I did simulation Ag, Au and Ni surfaces with MD. They dont take really that long. For about 100ps it is typically less than a day on RS6000 kind of machine. I am mainly a solvation dynamics guy worked most of my career with liquid simulations. Of course, I am familiar with the work that you publised with Ron Levy. Where are you located now? I thought you were working for some industry earlier at Boston. With warm regards Vijaya Kumar _____________________________________________________________________ There is plenty of simulations on bulk metals and precisely due to reason you've mentioned, doing it with DISACOVER or CHARMM is not a good idea IMHO. Metals usually have multi-bodu interactions and not very long-range interactions. I would try to write the MD code from the scratch. OIt's not that difficult you can actually start with examples >from let's say Allen & Tildesley or othe rsimulations textbook and use codes given thereas a starting point, all you would have to do is basically write your own force routine. As the interactions are not lon-ranged, using of neighbor lists or linked-cells will be very helpful. Hope this helps, Mike Michael J. Kotelyanskii _____________________________________________________________________ Hello, howard Please check the page of : Theoretical Division and Center For Nonlinear Studies, L.A.N.L., They did the massivley para. MD of metal crack. Dayong He _____________________________________________________________________ Dear Howard, My post-doc and I are studying Cu and Al (bulk, and with defects such as vacancies, surfaces, and grain boundaries) using two home-grown codes: VERNET (planewave pseudopotential electronic structure code) and pdQ (MD simulation). Both are oriented toward periodic (i.e. bulk) systems. VERNET is a parallel code, pdQ is in the process of being parallelized. We are also trying to develop improved (beyond EAM) force fields for these materials by 'normalizing' to the static electronic structure results. At present, pdQ is in too-primitive shape to release outside our group, but if you are interested in obtaining the code when it is ready for prime-time, I can add your name to the request list. (VERNET is currently being distributed under a beta-test agreement to interested parties). Regards, - Susan Atlas _____________________________________________________________________ I would recommend taking a look at Effective Medium Theory, which is a technique well suited for (essentially designed for) MD calculations on metals. A fairly nice, easy to use, implementation is available from: http://www.fysik.dtu.dk/~stoltze/artwork/artwork.html I hope this helps. -greg landrum _____________________________________________________________________ There has beed a reasonable amount of work on MD simulation of metals, which you will find in the solid-state physics literature. As you rightly say the forces in metals are not simply pairwise decomposable, and the main approaches are those of having a volume-dependent term, or of the embedded-atom or Finnis-Sinclair potentials. If you do a literature search for the works of Mike W. Finnis or check out his web site at Queens Uni, Belfast (probably www.qub.ac.uk) you will likely find some pointers. The potential-based approaches have had some modest success for nearly-free electron metals such as the alkali metals, but complex transition metals with all the effects of complex fermi surfaces strongly correlated electrons are a different kettle of fish. The intertwining of electronic and crystal structural properties characteristic of metals is one of the main reasons that most serious work in the field now uses ab-inito methods. I advise you to think carefully about what you hope to get out of the simulations and whether the models are up to delivering it. It's easy to come from the chemical/molecules world and imagine that pair and other potentials can be tweaked to give you an accurate model. In the world of solids that isn't necessarily so. Metals are much harder to model, and the Transition metals the most difficult of all. If you do go ahead with something like a Finnis-Sinclair potential, there may be some MD codes out there which handle embedded-atom style potentials, but you will almost certainly have to do some coding yourself. sincerely Keith Refson _____________________________________________________________________ My colleague Bob (R.A.) Johnson has spent his career working in metal simulations. I am in Ohio at the momnet but I can send you some references when I get home to VA. He uses the three and four body interactions in his own codes which are not any more difficult or time consuming than the molecular mechanics. I suggest you look into those types of calculations if you want beleivable results. Barry Farmer ____________________________________________________________________ -- Howard E. Alper, Ph.D. Dept. of Chemistry and The Advanced Materials Research Institute University of New Orleans New Orleans, LA 70148 504-280-7216 - Helping molecules find happiness for almost a 5th of a century. From David.Schrader@marquette.edu Mon May 4 15:28:51 1998 Received: from VMSE.CSD.MU.EDU for David.Schrader@marquette.edu by www.ccl.net (8.8.3/950822.1) id OAA11033; Mon, 4 May 1998 14:40:23 -0400 (EDT) Received: from vms.csd.mu.edu by vms.csd.mu.edu (PMDF V5.1-9 #27588) id <01IWMTVKQ9UOQUFSU9@vms.csd.mu.edu> for chemistry@www.ccl.net; Mon, 4 May 1998 11:25:44 CST Date: Mon, 04 May 1998 11:25:43 -0600 (CST) From: "David M. Schrader" Subject: Cusp-satisfying atomic orbitals To: chemistry@www.ccl.net Message-id: <01IWMTVKZDS2QUFSU9@vms.csd.mu.edu> X-VMS-To: IN%"chemistry@www.ccl.net" X-VMS-Cc: 6031SCHRADER MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Where can I find a collection of Roothaan-Hartee-Fock wave functions for atoms, the orbitals of which are constrained to exactly satisfy the electron-nuclear cusp conditions? =============================================================================== David M. Schrader Research Professor Department of Chemistry | Telephone numbers: Marquette University | (414) 288-3332 (office) P.O. Box 1881 | (414) 288-7066 (FAX) Milwaukee, WI 53201-1881, USA | (414) 288-3515 (secretary) E-mail: david.schrader@marquette.edu Web site: www.mu.edu/dept/chem/schrader.html ===============================================================================