From makula@citi2.fr Wed Nov 9 03:24:58 1994 Received: from FRMOP11.CNUSC.FR for makula@citi2.fr by www.ccl.net (8.6.9/930601.1506) id DAA23465; Wed, 9 Nov 1994 03:08:30 -0500 Received: from galaad.citi2.fr by FRMOP11.CNUSC.FR (IBM VM SMTP V2R2) with TCP; Wed, 09 Nov 94 09:08:09 EST Received: from bisance.citi2.fr by galaad.citi2.fr; (5.65/1.1.8.2/20Jun94-0455PM) id AA04250; Wed, 9 Nov 1994 08:59:31 +0100 Received: by bisance.citi2.fr (5.0/SMI-SVR4) id AA07153; Wed, 9 Nov 1994 09:07:25 --100 From: makula@citi2.fr (makula-bisance) Message-Id: <9411090807.AA07153@bisance.citi2.fr> Subject: chelation summary To: chemistry@ccl.net Date: Wed, 9 Nov 1994 09:07:24 +0100 (MET) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Content-Length: 4152 dear netters, some time ago, I asked the following question to the net. Here is a summary of the (few) answers I received. Thanks to all who answered ! Anyone wishing to add something else is welcome... original message : ****************************************************************************** I am looking for some information or references on the simulation of chelation of metallic ions by organic molecules, using either MM or QM methods. I will summarize for the net. Thanks, ****************************************************************************** now the answers : @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ You might want to have a look at the following reviews on MM and QM methods to study complexation with chelates : 1/ R.D. Hancock, and A.E. Martell, Chem. Rev., 89 (1989) 1875 " Ligand design for selective complexation of metal ions in aeqeous solution" 2/ Chantrell et al., Coord. Chem. Rev., 16 (1975) 259 Mainly of Porphyrins 3/ The whole issue of Coord. Chem. Rev., 118 (1992) Special issue 4/ Oleari et al., Coord. Chem. Rev., 1 (1966) 24 Semi-Empirical methods in coordination chemistry 5/ Brubaker et al., Coord. Chem. Rev., 53 (1984) 1 MM in coordination chemistry 6/ Hay, Coord. Chem. Rev., 126 (1993) 177 Idem 5 7/ Hancock, Acc. Chem. Res., 23 (1990) 253 MM and metal ion recognition 8/ Wipff, J. Coord. Chem., 27 (1992) 7 Molecular modeling in esp. crown-compounds 9/ Wipff et al., 1983, sorry do not have more info at hand, I'll look it up in my Mac, read it once... Some example calculations... 1/ Potassium and ethylenediamine MOLECULAR complexes Liau et al., JACS, 114 (1992) 9169 2/ Na+ and ethylenediamine Ikuta, Chem. Phys. Let., 116 (1985) 482 3/ Substituted 5-member chelate rings (diamine) Collogly et al., Inorg. Chem., 8 (1969) 1168 4/ Cd-EN EXCIPLEXES Takahashi et al., Chem. Phys. Let., 207 (1993) 379 Do you want macrocycles too ? Got some refs. I' m spending my whole year (from now till Oct. Next year) on complexes between earth-alkaline metal ions (Mg, Ca and Ba) and : ethyleneglycol ethylenediamine ethanedithiol propanediol (all 1,3 propanes) propanediamine propanedithiol Looks like I'm going to have fun^5. Hope I'll get to publish some things on this next year... Do send a summary to CCL, or to my E-mail address !!!!! Patrick Bultinck, University of Ghent, Sections Quantum chemistry and Macrocyclic Coordination chemistry. @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ You might look into papers and software by Vedani. The software is called YETI as I recall. I don't have any experience with it, but there is not that much out there to deal with mm and metals and most of that is just as vdw complexes. QM will require pseudo potentials for a 'standard' ab initio method or you might look into the DFT methods, as that is one area where they seem to have a clear advantage. ___________________________________________________________________________ M. Dominic Ryan (610)-270-6529 SmithKline Beecham Pharmaceuticals Internet: ryan%phmms0.mms@sb.com King of Prussia, PA @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ We have extended the MM2 force field for metalloporphyrins and cobalt corrinoids. In the case of the porphyrins, see J. Am. Chem. Soc., 114, 7218 (1992) and JCS Chem Commun, 1176 (1989). Two other papers on refinements for the iron porphyrins have been submitted. In the case of the cobalamins, two papers have been submitted. I'd be happy to send you copies of the submitted manuscripts if you wish. Regards, Helder Marques ------------------------------------------------------------ Prof. Helder M. Marques Department of Chemistry University of the Witwatersrand P.O. Wits 2050 Johannesburg South Africa Fax: Int + 27 + 11 + 339-7967 ------------------------------------------------------------ @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ Remi Le Goas CAMD Rhone-Poulenc Agrochimie Lyon - France E-mail : remi.le-goas@rp.fr From jig@qorg.unizar.es Wed Nov 9 04:25:03 1994 Received: from qorg.unizar.es for jig@qorg.unizar.es by www.ccl.net (8.6.9/930601.1506) id EAA23974; Wed, 9 Nov 1994 04:10:45 -0500 Message-Id: <199411090910.EAA23974@www.ccl.net> Received: by qorg.unizar.es (1.37.109.4/16.2) id AA29854; Wed, 9 Nov 94 10:08:55 GMT From: Jose Ignacio Garcia Subject: DeFT: Basis sets for S found! To: chemistry@ccl.net Date: Wed, 9 Nov 94 10:08:55 MET Mailer: Elm [revision: 70.85] Dear netters, It seems there is a complete agreement to recomend the WWW site: http://www.cray.com/apps/UNICHEM/Mainpage.html as the most adequate for finding DFT optimized basis sets. Incidentally, this information appeared in the net JUST before my request. I promise to read the messages carefully in the future in order to save bandwith. Many thanks to all people who reply to my request. Jose Ignacio ******************************************************************************* Dr. Jose Ignacio Garcia-Laureiro Phone : 34-(9)76-350475 Departamento de Quimica Organica Fax : 34-(9)76-567920 Instituto de Ciencia de Materiales de Aragon e-mail: jig@qorg.unizar.es C.S.I.C.-Universidad de Zaragoza jig@msf.unizar.es 50009 ZARAGOZA (SPAIN) ******************************************************************************* "And all this science I don't understand it's just my job five days a week..." ELTON JOHN - Rocket man ******************************************************************************* From chp1aa@surrey.ac.uk Wed Nov 9 05:25:08 1994 Received: from mail-server.surrey.ac.uk for chp1aa@surrey.ac.uk by www.ccl.net (8.6.9/930601.1506) id EAA24419; Wed, 9 Nov 1994 04:56:46 -0500 Received: from central.surrey.ac.uk by mail-server.surrey.ac.uk with SMTP (PP); Wed, 9 Nov 1994 09:56:36 +0000 Received: by central.surrey.ac.uk (1.37.109.8/16.2) id AA08552; Wed, 9 Nov 1994 09:56:15 GMT From: Mr Andrew D Allen Message-Id: <9411090956.AA08552@central.surrey.ac.uk> Subject: CCL: AMSOL Charges from AM1 SM2 To: chemistry@ccl.net Date: Wed, 9 Nov 94 9:56:15 GMT Mailer: Elm [revision: 70.85] Dear Netters, I have observed an increase of dipole, due to increases in the magnitude of the charge on atoms, in uridine 2'monophosphate. The details of my calculations are as follows:- Gas phase structure fully optimised using AM1 and POWELL method, to a gradient of 0.04 kcal/Ang. Aqueous phase structure is using the frozen gas phase geometry and AM1 SM2 with 1SCF. Relevant output:- Gas Phase Aqueous Phase Dipole moment (Debye) 12.80612 17.61578 Charges on PO3H P 2.5377 2.7478 O -1.1339 -1.2895 O -1.1467 -1.2316 O -0.8227 -0.8255 H 0.2381 0.2514 I was always lead to believe that an polar solvent stabilised the high charges on functional groups such as phosphates. Such that the magnitude of the charges was reduced, this would in theory reduce the dipole moment. Here however the magnitude of the charges has increased! Can anyone (Chris!) explain this? Andy ############################################################################### Structural and Computation Chemistry Group_________chp1aa@uk.ac.surrey - JANET. Department of Chemistry____________________________phone_______+44(483)-259591. University of Surrey_______________________________fax_________+44(483)-300803. Guildford, Surrey, GU2 5XH, UK_____________________ftp___________131.227.110.69 ############################################################################### From DFT95@FRMOP22.CNUSC.FR Wed Nov 9 06:25:03 1994 Received: from phem3 for DFT95@FRMOP22.CNUSC.FR by www.ccl.net (8.6.9/930601.1506) id GAA24858; Wed, 9 Nov 1994 06:16:38 -0500 From: Received: from FRMOP22.BITNET (MAILER@FRMOP22) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HJ9KGXNOY88YCJR8@phem3.acs.ohio-state.edu>; Wed, 9 Nov 1994 06:16:32 EST Date: Wed, 09 Nov 1994 12:14 +0000 Subject: DFT INTERNATIONAL CONFERENCE: PARIS 1995 To: "Ohio Supercomputer Center, Chemistry" Message-id: <"94-11-09-12:14:51.33*DFT95"@FRMOP22.CNUSC.FR> Content-transfer-encoding: 7BIT 6th INTERNATIONAL CONFERENCE ON THE APPLICATIONS OF THE DENSITY FUNCTIONAL THEORY IN CHEMISTRY AND PHYSICS AUGUST 29th - SEPTEMBER 1st 1995 PARIS (FRANCE) FIRST CIRCULAR The 6th edition of the International The SECOND CIRCULAR, containing Conference on the Applications of informations about registration the Density Functional Theory in fees, possible financial support Chemistry and Physics will be held in and accomodation, will be mailed Paris, August 29th - September 1st 1995. at the end of February 1995 to The meeting aims to bring together all who have returned the attached scientists interested in the basic pre-registration form before aspects of the theory, methodological January 15th 1995. developments and applications in The Scientific Program will include chemistry, biochemistry and physics. plenary lectures, oral contributions and a poster session. To receive the next mailing, return the questionnaire by mail or fax to: Dr. A. Goursot Ecole de Chimie 8, rue de l'Ecole Normale 34053 Montpellier, Cedex France fax: (33)-67 14 43 49 e-mail: dft95@frmop22.cnusc.fr The following speakers have already Scientific Committee agreed to present an invited paper: A. Bencini, Univ. Firenze (I) A. St-Amant (Canada) C. Daul, Univ. Fribourg (CH) E. J. Baerends (The Netherlands) W. Kohn, Univ. California (USA) R. Car (Switzerland) J. A. Pople, Northwestern Univ. (USA) D. Case (U.S.A.) N. Russo, Univ. Calabria (I) M. Cohen (U.S.A.) V. Smith, Queen's Univ. (CA) P. Fantucci (Italy) T. Ziegler, Univ. Calgary (CA) B. Johnson (U.S.A) M. Levy (U.S.A.) Organizing Commette R. Parr (U.S.A) M. Allavena, Univ. Paris VI J. Perdew (U.S.A.) C. Bureau, CEA, Paris D. Salahub (Canada) H. Chermette, Univ. Lyon I K. Schwartz (Austria) A. Goursot, ENSC, Montpellier C. Umrigar (U.S.A) J. Langlet, Univ. Paris VI J. Weber (Switzerland) C. Mijoule, Univ. Paris VI W. Yang (U.S.A.) A. Savin, Univ. Paris VI Complementary information can also be asked to: H. Chermette: cherm@frcpn11.in2p3.fr A. Goursot: dft95@frmop22.cnusc.fr C. Mijoule: cm@dim.jussieu.fr _____________________________________________________ DFT 95 pre-registration form Paris, August 29 - September 1, 1995 Name Affiliation Address Fax E-mail Probability of attending 90% 50% 10% Number of accompanying persons Wish to present poster Yes No oral Yes No From h.rzepa@ic.ac.uk Wed Nov 9 08:25:03 1994 Received: from punch.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.9/930601.1506) id HAA25462; Wed, 9 Nov 1994 07:30:27 -0500 Received: from sg1.cc.ic.ac.uk by punch.ic.ac.uk with SMTP (PP) id <03957-0@punch.ic.ac.uk>; Wed, 9 Nov 1994 12:28:30 +0000 Received: from macb.ch by cscmgb.cc.ic.ac.uk (931110.SGI/4.0) id AA12666; Wed, 9 Nov 94 12:29:55 GMT X-Sender: rzepa@sg1.cc.ic.ac.uk Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 9 Nov 1994 12:29:55 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Rzepa,Henry) (Rzepa,Henry) Subject: chemical MIME discussion group Some of you may remember the postings from me about 8 months ago on chemical MIME types. These eventually coalesced into an Internet Draft, which ran from May - October. It is now expired, and needs to be revised. The revision group is currently myself, Peter Murray-Rust and Ben Whitaker. In order to make things more democratic, I have set up a listserver for the group. You are invited to subscribe to it, if you have an interest in standardising the way chemistry and the Internet interact. We do hope however to keep the group fairly focussed on this area. Send a 1 liner to listerver@ic.ac.uk containing the message subscribe chemime your name (no signatures please, they only confuse the listserver). We hope to automatically convert any postings to this group into on-line HTML style documents (with subscribers agreement). If you do not wish to contribute to discussions, you should still be able to see what others have written without subscribing to the group (I know that the current proliferation of discussion lists results in more mail than I can cope with! I would not wish to make things worse for you all!!) The first aim of the group will be to produce a second IETF draft on chemical MIME types, which would run for a further 6 months. This should be followed by a IETF RFC, which would be a standards-track document. We may also wish to consider other standard documents, as for example SGML type "dtds" in this area. Dr Henry Rzepa, Department of Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 2.1.1, Tel (44) 171 594 5774 or 594 5809. Fax: (44) 171 594 5804. World-Wide-Web URL: http://www.ch.ic.ac.uk/rzepa.html From gotwals@mcnc.org Wed Nov 9 09:25:03 1994 Received: from robin.mcnc.org.mcnc.org for gotwals@mcnc.org by www.ccl.net (8.6.9/930601.1506) id JAA27148; Wed, 9 Nov 1994 09:14:39 -0500 Received: from [128.109.178.39] by robin.mcnc.org.mcnc.org (8.6.9/MCNC/8-10-92) id JAA01562; Wed, 9 Nov 1994 09:14:38 -0500 for Message-Id: <199411091414.JAA01562@robin.mcnc.org.mcnc.org> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 9 Nov 1994 09:18:14 +0500 To: chemistry@ccl.net, CHEMED-L%UWF.BITNET@uga.cc.uga.edu From: gotwals@mcnc.org (Bob Gotwals) Subject: Correction to Workshop posting Two instructor names for the January Molecular Modeling and Drug Design Workshop, to be held at the North Carolina Supercomputing Center (RTP, NC), were misprinted. Correct names and organizations are: K. Raghavan Biosym Technologies, Inc. Scott Kahn Molecular Simulations Inc. From kris@bionmr1.rug.ac.be Wed Nov 9 10:25:10 1994 Received: from mserv.rug.ac.be for kris@bionmr1.rug.ac.be by www.ccl.net (8.6.9/930601.1506) id JAA27868; Wed, 9 Nov 1994 09:42:04 -0500 Received: from bionmr1.rug.ac.be by mserv.rug.ac.be with SMTP id AA18245 (5.67b/IDA-1.5 for <@mserv.rug.ac.be:CHEMISTRY@ccl.net>); Wed, 9 Nov 1994 15:40:48 +0100 Received: by bionmr1.rug.ac.be (931110.SGI/931108.SGI.AUTO.ANONFTP) for @mserv.rug.ac.be:h.rzepa@ic.ac.uk id AA01941; Wed, 9 Nov 94 15:39:42 +0100 From: "Kris Boulez" Message-Id: <9411091539.ZM1939@bionmr1.rug.ac.be> Date: Wed, 9 Nov 1994 15:39:39 +0100 In-Reply-To: h.rzepa@ic.ac.uk (Rzepa,Henry) (Rzepa,Henry) "CCL:chemical MIME discussion group" (Nov 9, 12:29pm) References: X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: CHEMISTRY@ccl.net Subject: Re: CCL:chemical MIME discussion group Cc: h.rzepa@ic.ac.uk Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Nov 9, 12:29pm, Rzepa,HenryRzepa,Henry wrote: > Subject: CCL:chemical MIME discussion group [...] > the way chemistry and the Internet interact. We do hope however to keep the > group fairly focussed on this area. Send a 1 liner to > listerver@ic.ac.uk containing the message should be listserver@ic.ac.uk ^ > subscribe chemime your name > > Dr Henry Rzepa, Department of Chemistry, Imperial College, LONDON SW7 2AY; > rzepa@ic.ac.uk via Eudora 2.1.1, Tel (44) 171 594 5774 or 594 5809. > Fax: (44) 171 594 5804. World-Wide-Web URL: > http://www.ch.ic.ac.uk/rzepa.html > > Kris, -- Kris Boulez (Kris.Boulez@rug.ac.be) Biomolecular NMR unit University of Ghent, Belgium From FS300627@Sol.YorkU.CA Wed Nov 9 13:25:07 1994 Received: from Sol.YorkU.CA for FS300627@Sol.YorkU.CA by www.ccl.net (8.6.9/930601.1506) id MAA01936; Wed, 9 Nov 1994 12:50:40 -0500 From: Received: from Sol.YorkU.CA by Sol.YorkU.CA (PMDF V4.3-7 #6007) id <01HJ9Y75Y90G019BDF@Sol.YorkU.CA>; Wed, 9 Nov 1994 12:50:27 EST Date: Wed, 09 Nov 1994 12:50:27 -0500 (EST) Subject: X-Ray Crystallography display To: chemistry@ccl.net Message-id: <01HJ9Y75ZUW2019BDF@Sol.YorkU.CA> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Greetings, A collegue of mine has the following problem. His X-ray crystallography apparatus comes with a software program called SHELLX (I believe this comes from Siemens, Holland). Within SHELLX there is a program called XP (interactive molecular graphics v4.2) which creates *.res output files. However, for what ever reason, there is no graphics display program associated with SHELLX. The question now is, does anybody know of a simple molecular display package that can read the *.res files, diplay them properly, rotate them, measure distances, angles etc. No manipulation of the molecule is nessecary. Thanx in advance, Patrick M. van der Valk, M.Sc ************************************************************************** ** Patrick van der Valk | It is a capital mistake to theorize * ** BioMimic | before one has data. Insensibly one * ** | begins to twist facts to suit theories * ** e-mail:FS300627@Sol.YorkU.Ca | instead of theories to suit facts. * ** Phone: (416) 736-5747 | * ** Fax: (416) 650-3558 | -Sherlock Holmes- * ************************************************************************** From blonski@alumina.rutgers.edu Wed Nov 9 15:26:23 1994 Received: from alumina.rutgers.edu for blonski@alumina.rutgers.edu by www.ccl.net (8.6.9/930601.1506) id PAA04869; Wed, 9 Nov 1994 15:20:29 -0500 Received: by alumina.rutgers.edu (5.59/SMI4.0/RU1.5/3.08) id AA07148; Wed, 9 Nov 94 15:20:14 EST From: blonski@alumina.rutgers.edu (Slawomir Blonski) Message-Id: <9411092020.AA07148@alumina.rutgers.edu> Subject: Re: MD or MC To: chemistry@ccl.net Date: Wed, 9 Nov 1994 15:20:13 -0500 (EST) In-Reply-To: <9411081657.AA08549@cyclone.ERE.UMontreal.CA> from "Hinsen Konrad" at Nov 8, 94 11:57:20 am X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1294 Q: > Which one, MD or MC, you will select if CPU time-constraint > is imposed ? A: > The choice between MD and MC depends not on your CPU time allocation, > but on the problem you want to solve. There is a class of Monte Carlo simulations which can be directly compared with molecular dynamics. These are the MC studies of time-dependent phenomena. See for example works on polymer reptation by Kurt Binder or on biopolymers by team Skolnick - Kolinski. In such an approach, a new MC configuration is formed from the previous one (after being accepted with Metropolis criterion). This may be assumed to be equivalent to a time evolution of the system. Because changes in the system between consecutive MC configurations are greater than after a single MD time step, one can treat the MC step as a time period much longer than the MD time step. In this way, the time-dependent MC simulations extend longer in time than the MD with the same number of steps, although the exact length of the MC time step is hard to estimate and MC gives only positions of the particles, but not the momenta. However, MC may be preferred over MD, if one simulates large systems with long relaxation times which are beyond reach of current computers. Slawomir Blonski PS. I use molecular dynamics. From PADMEEKS@UKCC.UKY.EDU Wed Nov 9 16:25:08 1994 Received: from UKCC.uky.edu for PADMEEKS@UKCC.UKY.EDU by www.ccl.net (8.6.9/930601.1506) id PAA05454; Wed, 9 Nov 1994 15:50:34 -0500 Message-Id: <199411092050.PAA05454@www.ccl.net> Received: from UKCC.UKY.EDU by UKCC.uky.edu (IBM VM SMTP V2R2) with BSMTP id 8628; Wed, 09 Nov 94 15:49:57 EST Received: from ukcc.uky.edu (NJE origin PADMEEKS@UKCC) by UKCC.UKY.EDU (LMail V1.2a/1.8a) with BSMTP id 6755; Wed, 9 Nov 1994 15:49:56 -0500 Date: Wed, 09 Nov 94 15:46:45 EST From: Jim Meeks Subject: SUN Workstation To: CHEMISTRY@ccl.net I need some information on a SUN Workstation, Model IPC, 19" Monitor, 400 MB HD --what is the approximate value? What could be a possible age? Thank you. ========================================================================= James L. Meeks | Telephone: 502 554 9200 X189 Department of Physics | : 502 554 6214 Paducah Community College | FAX: 502 554 6214 PADUCAH, KY 42002-7380 | INTERNET: PADMEEKS@UKCC.UKY.EDU | COMPUSERVE: 72114,3460 ========================================================================= From arne@hodgkin.mbi.ucla.edu Wed Nov 9 17:25:18 1994 Received: from hodgkin.mbi.ucla.edu for arne@hodgkin.mbi.ucla.edu by www.ccl.net (8.6.9/930601.1506) id QAA06288; Wed, 9 Nov 1994 16:51:56 -0500 Received: by hodgkin.mbi.ucla.edu; id AA18558; Wed, 9 Nov 1994 13:56:49 -0800 Message-Id: <9411092156.AA18558@hodgkin.mbi.ucla.edu> To: chemistry@ccl.net Subject: Re: MD or MC Date: Wed, 09 Nov 94 13:56:48 -0800 From: "Arne Eofsson (arne@uclaue.mbi.ucal.edu)" X-Mts: smtp >Q: >> Which one, MD or MC, you will select if CPU time-constraint >> is imposed ? >A: >> The choice between MD and MC depends not on your CPU time allocation, >> but on the problem you want to solve. > >There is a class of Monte Carlo simulations which can be directly compared >with molecular dynamics. These are the MC studies of time-dependent phenomena. >See for example works on polymer reptation by Kurt Binder or on biopolymers >by team Skolnick - Kolinski. In such an approach, a new MC configuration is >formed from the previous one (after being accepted with Metropolis criterion). >This may be assumed to be equivalent to a time evolution of the system. Because >changes in the system between consecutive MC configurations are greater than >after a single MD time step, one can treat the MC step as a time period much >longer than the MD time step. In this way, the time-dependent MC simulations >extend longer in time than the MD with the same number of steps, although >the exact length of the MC time step is hard to estimate and MC gives only >positions of the particles, but not the momenta. However, MC may be preferred >over MD, if one simulates large systems with long relaxation times which are >beyond reach of current computers. I would like to point out some important facts about these type of simulations. 1. A direct comparison is not possible, Skolnick/Kolinski did some comparisons between their (lattice) MC simulations with brownian dynamics simulations and claimed that their detailed lattice models where about 2-4 times faster (Kolinki, et al 1994, Proteins). However Karplus pointed out that the time step used in their brownian dynamics simulations was too long. (These are just some few problems that can occur) 2. The dynamics that you do in a MC might be very dependent on the type of step you allow. You might favor the formation of helixes over sheets and so on. 3. I can do things in a MC simulation that I would never be able to in MD (For instance I can get a protein starting from a random conformations to be folded into a compact structure under the AMBER potential in a day or two on a workstation). This woud take much longer with MD. I haven't tried but I think so. 4. In MC I can use energy functions without being able to take their derivative. (very usefull in some cases) 5. In MC I can put on any constrraints that I want to. 6. Usually for a detailed description (of a protein) and a detailed (amber) energy function MD is more accurate (my guess) arne ****************************************************************************** ** From: Arne Elofsson ** ** Fax: +1-(310)-206-3914 or Fax: +1-(310)-206-7286 ** ** Tel: +1-(310)-825-1402 ** ** ** ** Email: arne@hodgkin.mbi.ucla.edu (arne@uclaue.mbi.ucla.edu) ** ** ** ** Adress: Molecular Biology Institute Home: 1370 Veteran #311 ** ** 405 Hilgard Avenue, UCLA Los Angeles ** ** Los Angeles CA 90024 ** ** 90024-1570 California USA ** ** USA Tel: +1-(310)-268-8006 ** ****************************************************************************** From bruce@dggin1.utmb.edu Wed Nov 9 18:25:10 1994 Received: from dggin1.utmb.edu for bruce@dggin1.utmb.edu by www.ccl.net (8.6.9/930601.1506) id RAA06999; Wed, 9 Nov 1994 17:30:11 -0500 Received: by dggin1.utmb.edu (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA14393; Wed, 9 Nov 94 16:34:23 -0600 From: "Bruce A. Luxon" Message-Id: <9411091634.ZM14391@dggin1.utmb.edu> Date: Wed, 9 Nov 1994 16:34:16 -0600 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: Biomolecular NMR & Comp Chem WWW page Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 CCL Netters, We are announcing the introduction of our NMR and Computational Chemistry WWW home page. The URL is - http://www.nmr.utmb.edu/ We have links for a wide variety of interests and we distribute our MORASS Hybrid Matrix NOE structural refinement software from there as well. Hopefully many of you will find this helpful. Bruce From iuliu.hossu@canrem.com Wed Nov 9 22:25:15 1994 Received: from seraph.uunet.ca for iuliu.hossu@canrem.com by www.ccl.net (8.6.9/930601.1506) id VAA09711; Wed, 9 Nov 1994 21:55:29 -0500 Received: from portnoy.canrem.com ([198.133.42.251]) by mail.uunet.ca with SMTP id <87763-5>; Wed, 9 Nov 1994 21:55:48 -0500 Received: from canrem.com by portnoy.canrem.com (4.1/SMI-4.1) id AA05783; Wed, 9 Nov 94 21:51:54 EST Received: by canrem.com (PCB-UUCP 1.1f) id 1BDB11; Wed, 9 Nov 94 21:39:55 -0400 To: chemistry@ccl.net Reply-To: CRSO.CompChemistry@canrem.com Sender: CRSO.CompChemistry@canrem.com Subject: CHEMICALS FOR PROJECT From: iuliu.hossu@canrem.com (Iuliu Hossu) Message-Id: <60.3456.6509.0C1BDB11@canrem.com> Date: Wed, 9 Nov 1994 20:03:00 -0500 Organization: CRS Online (Toronto, Ontario) HHHHHEEEEEEEEEEEEELLLLLLLLLLLLLLLLPPPPPPPPP !!!!!!!!!!!!!!! I am a grade twelve student doing my Chemistry OAC project on crystallography. I REALLY need the following chemicals, and it seems that I cannot find them anywhere. A teacher told me that the school cannot give me any chemicals, and that you need a licence to buy chemicals. The book that I am using said that I could get every one of these chemicals through a pharmacy, but the pharmacist glanced over my sheet in two seconds saying he was not into chemicals. Your help would be GREATLY appreciated. 135.4g Potassium Aluminum Dodecahydrate ( Alum ) 122.9g Potassium Chromium Dodecahydrate ( Chrome Alum ) 485g Potassium Sodium Tartrate Tetrahydrate ( Rochelle Salt ) 530g Nickel Sulfate Hexahydrate 81g Nickel Sulfate Heptahydrate 235.8g Sodium Bromate 470g Sodium Chlorate 466g Sodium Nitrate ( Niter, Saltpeter are confusingly used for both Sodium Nitrate and Potassium Nitrate. ) 93g Potassium Ferricyanide ( Red Prussiate of Potash ) 20g Copper Acetate Monohydrate 10cc Acetic Acid 18.5cc 88% formic acid 29.5g Strontium Carbonate 60g Sodium Dichromate Dihydrate 7.5g Lithium Carbonate 8g Sodium Hydroxide 22.5g powdered Calcium Oxide 48g Glacial Acetic Acid 20g Copper Acetate Monohydrate