From rozas@pinar1.csic.es Mon Nov 24 06:35:09 1997 Received: from pinar.csic.es for rozas@pinar1.csic.es by www.ccl.net (8.8.3/950822.1) id GAA02106; Mon, 24 Nov 1997 06:20:08 -0500 (EST) Received: from pinar.csic.es by pinarvms.csic.es (PMDF V5.1-4 #13290) id <01IQDYXYSY40001MPH@pinarvms.csic.es> for CHEMISTRY@www.ccl.net; Mon, 24 Nov 1997 12:20:34 CE X400-Received: by /PRMD=iris/ADMD=mensatex/C=es/; Relayed; Mon, 24 Nov 1997 12:18:38 +0000 Date: Mon, 24 Nov 1997 12:18:38 +0000 From: Isabel Rozas Subject: Basis sets for Sn To: CHEMISTRY@www.ccl.net Message-id: <904*rozas@pinar1.csic.es> Content-identifier: 904 MIME-version: 1.0 (Generated by Ean X.400 to MIME gateway) X400-Content-type: P2-1984 (2) X400-MTS-identifier: [/PRMD=iris/ADMD=mensatex/C=es/;971124121838] X400-Originator: rozas@pinar1.csic.es X400-Recipients: non-disclosure:; Hi there! I am looking for basis sets for Sn. I found the STO-3G and the 3-21G basis sets but I would need something a little bigger. Does anybody know where I can get them? or Does anybody have them available somewhere? Thanks in advance, Isabel Rozas ----------------------------------------------------------------------- Isabel Rozas ROZAS@PINAR1.CSIC.ES Instituto de Quimica Medica (C.S.I.C.) Phone: 34-1-562 2900 c/ Juan de la Cierva 3 Fax: 34-1-564 4853 28003-Madrid (Spain) ----------------------------------------------------------------------- From zuilhof@Sg1.OC.WAU.NL Mon Nov 24 09:35:10 1997 Received: from net.wau.nl for zuilhof@Sg1.OC.WAU.NL by www.ccl.net (8.8.3/950822.1) id JAA03160; Mon, 24 Nov 1997 09:03:47 -0500 (EST) Received: from SG1.OC.WAU.NL by NET.WAU.NL (PMDF V5.1-9 #23446) with SMTP id <01IQE4MWG9PA001TG6@NET.WAU.NL> for CHEMISTRY@www.ccl.net; Mon, 24 Nov 1997 15:03:27 GMT +0100 Received: from [137.224.136.38] by SG1.OC.WAU.NL via SMTP (931110.SGI/930416.SGI) for @Net.WAU.NL:CHEMISTRY@www.ccl.net id AA05540; Mon, 24 Nov 1997 15:02:47 +0100 Date: Mon, 24 Nov 1997 15:02:47 +0100 From: zuilhof@Sg1.OC.WAU.NL (Han Zuilhof) Subject: Re: Basis sets for Sn?: downloadable from EMSL website To: Isabel Rozas , CHEMISTRY@www.ccl.net Message-id: MIME-version: 1.0 Content-type: text/plain; charset="us-ascii" At 12:18 PM 11/24/97, Isabel Rozas wrote: >Hi there! >I am looking for basis sets for Sn. I found the STO-3G and >the 3-21G basis sets but I would need something a little >bigger. >Does anybody know where I can get them? or Does anybody >have them available somewhere? >Thanks in advance, > > Isabel Rozas Dear Isabel, A more substantial double zeta DFT basis set is available for Sn on the EMSL website, from which it can be downloaded. http://wserv1.dl.ac.uk:800/emsl_pnl/basisform.html I've recently started to use it, and it yields nice results, which deviate significantly from the 3-21G** basis. Best regards, Han Zuilhof ______________________________________________________________________ Han Zuilhof | E-mail: ZUILHOF@SG1.OC.WAU.NL Laboratory of Organic Chemistry | FAX : 31-317-484914 Department of Biomolecular Sciences | phone : 31-317-482367 Wageningen Agricultural University | Dreijenplein 8 | 6703 HB Wageningen | "Excite a photochemist!" The Netherlands | From malisa@nirvana.uncor.edu Mon Nov 24 11:35:13 1997 Received: from nirvana.uncor.edu for malisa@nirvana.uncor.edu by www.ccl.net (8.8.3/950822.1) id KAA04699; Mon, 24 Nov 1997 10:38:41 -0500 (EST) Received: (from malisa@localhost) by nirvana.uncor.edu (8.7.5/8.7.3) id NAA00205 for CHEMISTRY@www.ccl.net; Mon, 24 Nov 1997 13:22:26 GMT Date: Mon, 24 Nov 1997 13:22:26 GMT From: Malisa Chiappero Message-Id: <199711241322.NAA00205@nirvana.uncor.edu> To: CHEMISTRY@www.ccl.net Subject: g94 LS coupling Hi! I am studying the iodine LS coupling, and I would want make some calculaltions with g94, but the program havn't the Zeff for atom 53. Are there any possibility to incorporate this value in any external archive? and which is this value?. Is it possible to use GAMESS Zeff? Any suggestions are welcomed ? Malisa From chemtw@showme.missouri.edu Wed Nov 19 16:34:10 1997 Received: from mail.missouri.edu for chemtw@showme.missouri.edu by www.ccl.net (8.8.3/950822.1) id PAA11726; Wed, 19 Nov 1997 15:37:27 -0500 (EST) Received: from black.missouri.edu (black.missouri.edu [128.206.2.222]) by mail.missouri.edu (8.8.5/8.8.5) with ESMTP id OAA155666 for ; Wed, 19 Nov 1997 14:37:17 -0600 Received: from localhost (chemtw@localhost) by black.missouri.edu (8.8.5/8.8.5) with SMTP id OAA22396 for ; Wed, 19 Nov 1997 14:36:42 -0600 X-Authentication-Warning: black.missouri.edu: chemtw owned process doing -bs Date: Wed, 19 Nov 1997 14:36:42 -0600 (CST) From: Troy Wymore X-Sender: chemtw@black.missouri.edu To: chemistry@www.ccl.net Subject: N-H Correlation function in CHARMM Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I would like to construct a correlation function for N-H vectors in my peptide from trajectory files using CHARMM version 24b2. People have done this to make the connection between the motion of the peptide and NMR relaxation. I know CHARMM has the NMR analysis facility which I have used successfully; my problem is using CORREL to construct the correlation function. My question is this: Do I have to rewrite the coordinate trajectory files so that the peptide is oriented with respect to some reference structure or can I just put in something like : trajectory firstu 50 nunit 1 begin 779750 stop 809500 skip 250 - orient select type CA end (just an example) If anyone can supply an example script where they did a similar sort of analysis; especially for N-H vectors in proteins/peptides, it would be appreciated. I figured that my script should be close to the one described in the docs for fluorescence depolarization, but something is still wrong. Any help would be much appreciated. **************************************** Troy Wymore Department of Chemistry University of Missouri-Columbia Columbia, MO 65211 e-mail: chemtw@showme.missouri.edu ***************************************** From youkha@inpharmatics.com Wed Nov 19 22:41:36 1997 Received: from inet1.inetworld.net for youkha@inpharmatics.com by www.ccl.net (8.8.3/950822.1) id WAA13466; Wed, 19 Nov 1997 22:16:30 -0500 (EST) Received: from sydney.inpharma.com (n209060174003.inetworld.net [209.60.174.3] (may be forged)) by inet1.inetworld.net (8.8.7/8.8.7) with SMTP id TAA22648; Wed, 19 Nov 1997 19:16:22 -0800 (PST) Message-ID: <34739BE8.1383@inpharmatics.com> Date: Wed, 19 Nov 1997 18:09:44 -0800 From: Philippe Youkharibache Reply-To: youkha@inpharmatics.com Organization: InPharmatics Corp. X-Mailer: Mozilla 3.01Gold (Win95; I) MIME-Version: 1.0 To: Dan Strahs CC: CHEMISTRY@www.ccl.net Subject: Re: CCL:visualizing normal modes? References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dan Strahs wrote: > > I'm trying to visualize some the normal mode eigenvectors for systems I've > been working with. > > I have a number of options, but none really satisfy me. > > a) I can use Insight/Biosym/MSI to draw arrows attached to the atom > positions; but this is an extraordinarily crude approach. It also requires > me to iteratively read in and delete the objects associated with the > particular mode I want to consider. > .... > Is there some package (preferably free) which will: > > 1) Display atoms and eigenvectors in a 3-D, rotatable reference > frame; > 2) Allow me to import the entire calculated set of normal modes > and visualize them individually without progressive reloads; > > 3) Generate some form of output (i.e. Postscript) > > Thanks for any help that can be offered in this regard. Dan, First of all, for a repetitive task in InsightII you can use BCL MACROS. There should be one available and floating around to precisely visualize normal modes. As you said though it is not a viable solution if you have hundreds of vectors and if you want to animate them. I don't know if you know about DeCipher which is completely integrated to InsightII There are ways of doing that - with the latest release that is about to ship (version 97). This is essentially a version of the MSDA-DeCipher software version 4.1 that we developed for Bristol-Myers-Squibb early 1995 while I was still at Biosym :-(. What you could do is the following (on top of my head after two years of not even touching the software - so give a +/-), and this is BTW a general back-door to all types of external data import. Since DeCipher is a toolkit you'll have a few definition steps and then it should be a brise. You will not have to know anything else than to use a spreadsheet (a minimum) and define mathematical functions (no programming, no looping at all). 1/ Read in a text file containing your vectors on an atom basis - in a spreadsheet -. You could read in any set of scalars, vectors and even tensors on an atom basis (row) -AND- frame basis if you have an animation (note that there is a transpose command if needed). 2/ define a muldidimensional numerical function "normal_modes" (numeric) of type "vector" (first row of spreadsheet atom1.xyz, atom2.xyz ..., then optionally one row per frame if you read-in a trajectory, which would have to be in a supported format). What a numerical function does is to attach a number or set of numbers (vectors, tensors) to each atom (or residue or molecule as a matter of fact (use option). Use the option Map_To_Molecule (the fact is that you can map on any point in space). Normally (if there are no bugs !) they should then rotate with the molecule. For normal modes it is just a matter of considering each mode associated to a frame. For that the only issue is to read in a synthetic trajectory of 3N-6 frames that can be all identical to the equilibrium (or not) structure you used for the calculation, as DeCipher does not know specifically of normal modes. The other way around, more satisfactory if you have just a few modes is to define a function per mode, you can then display them one at a time or simultaneously (see hereafter) on the same structure. 3/ Create a multi-dimensional vector object (or an object in the Insight sense with atom based vector components representing normal modes. you define a geometrical object (called geometrics in DeCipher) in your case a "Vector" with the From_Function option, specifying the "normal_mode" function you've just defined. You end up with ONE object representing an atom-based vector function, this object is dynamic so if the molecule is animated AND normal modes have been read, you can browse through normal modes. Warning: you should check if functions and geometrics are saved with say a .psv file. Note also that you can change the numbers in the spreadsheet, the function will update and so will the vector ... this is a dynamic information system. Properties can be expressed formally as functions of atomic variables and are recomputed (or re-looked up) dynamically. Also if you define functions of these normal modes, they'll be updated dynamically in a table or on the molecule. 4/ Printing Well the good news is that it should now print as anything else in Insight (I hope it's true). I know it might sound esoteric to those of you who have been using DeCipher in previously released version, which sadly really dates 1993. I am the first one to be sorry that this software has not been released before, although I made it available to a small group thanks to the generosity of Bristol-Myers-Squibb early 1995. I just hope you can put your hands on it soon, and I have been told that it is shipping now. Good Luck. Philippe Youkharibache -- ======================================================================= Philippe Youkharibache, Ph.D. InPharmatics Corp. e-mail: youkha@inpharmatics.com 11440 W. Bernardo Court, Suite 300 tel: (619) 530 8550 San Diego, CA 92127 fax: (619) 530 8555 ======================================================================= From mealli@service.area.fi.cnr.it Thu Nov 20 03:34:17 1997 Received: from cioccolata.issecc.fi.cnr.it for mealli@service.area.fi.cnr.it by www.ccl.net (8.8.3/950822.1) id DAA14429; Thu, 20 Nov 1997 03:25:46 -0500 (EST) Received: from pentium3.issecc.fi.cnr.it by cioccolata.issecc.fi.cnr.it; (5.65v3.2/1.1.8.2/17Sep96-0948AM) id AA29311; Thu, 20 Nov 1997 10:41:46 +0100 From: Carlo Mealli To: "E. Lewars" Cc: chemistry@www.ccl.net Subject: Re: CCL:EHM TODAY--OPINIONS Message-Id: Date: Thu, 20 Nov 1997 09:25:30 -0500 (EST) Priority: NORMAL X-Mailer: Simeon for Windows X-Authentication: none Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Transfer-Encoding: QUOTED-PRINTABLE On Wed, 12 Nov 1997 16:22:51 -0500 (EST) "E. Lewars" =0A wrote: > >Wed, 1997 Nov 12 > >>From E. Lewars >To: CCL >Subj: Extended Hueckel Today--opinions > >Hello, What do people out there in netland think of the *current* status = of =0Athe >extended Hueckel method that was popularized by Roald Hoffmann, starting >ca. 1963? It was, I think, the first generally applicable method, in the >sense that it was not limited to planar pi electron arrays and could in >principle perform geometry optimizations. Is it the general view that it = is >essentially obsolete, having been displaced by more sophisticated methods = =0Alike >MNDO and its decendants AM1 and PM3? Does it have some advantages =0Aover= AM1 >and PM3? > >Thanks > E. Lewars >=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Almost as an hobby and also thanks to the help of some enthusiastic =0Ac= ollaborators (first of all Dr. D.M.Proserpio), I have long worked to develo= p =0Aa handy graphic interface (package CACAO) to the numerical results of = ehmo =0Acalculations (the basic programs of Roald Hoffmann at Cornell).=20 I am very much aware of the shortcomings of the method in terms of highly = =0Areliable quantitative results. Mainly, the problems arise from neglectin= g the =0Ainter-electronic terms. Under these circumstances it is impossible= to trust =0Ablindly a quantitative response associated, for example, with = geometry =0Aoptimization or with the energetics of an electronic transition= .=20 Still most of the times "the trends" are correct and there is a lot to l= earn from =0Atrends! If used "cum grano salis" (i.e. always referring to th= e common =0Aconcepts of chemical bonding, stereochemistry and reactivity), = the method =0Aprovides a lot of quick, useful and reliable information. The= rigourous =0Asubdivision of the MOs in terms of symmetry properties (remem= ber the =0Arelevance of the Conservation of Orbital Symmetry ideas expresse= d by Roald =0AHoffmann) is dense of chemical meanings. Thus, if a low symme= try molecule is =0Aanalyzed starting from the conformer with the highest po= ssible symmetry, the =0Aevolution of the MOs and the redistribution of the = electrons in them do almost =0Ainvariably point toward the correct solution= . Moreover it is clearly seen where =0Athe electronic problems arise from i= n the conformers with higher symmetry. In =0Aother words, the Perturbation = Theory works well and the ehmo method helps =0Ato interpret it beautifully.= =20 Nowadays with the ubiquitous PCs, it is fast and easy to perform these = =0Acalculations at will and to explore many different deformational trends = and/or =0Areaction pathways. The graphics more than the pure numbers are th= e helpful =0Ainterpretational tool and also the non-specialists (the experi= mental chemists, =0Athe teachers, the students, etc.) can now seek a suited= MO description of the =0Achemical bonding in a molecule or series of molec= ules. But there is a good =0Apoint to continue to exploit the ehmo method= also for those who perform high =0Alevel theoretical studies. My viewpoint is that ehmo=20 cannot be substitutive but is a coadjutant of the latter methods most of wh= ich =0A(from AM1 on) provide no interpretational tools, no eventual insight= to the =0Auser. As in an explorative approach, a preliminary ehmo analysis= sheds light in =0Athe field where the higher level computations are meant = to be=20 performed. Moreover, I notice myself from comparisons that the basic =0Aqua= ntitative results are very often consistent. For example, the frontier MOs = =0Afrom the ehmo and those from accurate ab-initio methods correspond in = =0Aenergy order, symmetry and composition. When this is the case, one can = =0Astrategically use the ehmo method to interpret to basic underpinnings of= the =0Agiven quantitative result. Beside the list of geometrical parameter= s of an =0Aoptimized geometry, the chemist needs to know the electronic fac= tors which =0Aaffect the latter in order to understand the role, say, of so= me substituents. The =0Aultimate goal of theory is to favour the planning o= f new experiments. =85Much chemistry has been interpreted in the past 20-30 years thanks to th= e =0Aehmo method because it is a powerful telescope to see Perturbation the= ory at =0Awork. In my opinion ehmo cannot be dismissed as obsolete especial= ly now =0Athat personal computers allow to construct a MO description of ch= emical =0Abonding almost as easily as the Valence Bond description is const= ructed by =0Ausing paper and pencil. Dr. Carlo Mealli =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 Dr. Carlo Mealli ISSECC - CNR, Via Nardi 39, 50132 Firenze, Italy Tel 0039-55-2346653, Fax 2478366 e-mail: mealli@cacao.issecc.fi.cnr.it =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 From tf004873@psinet.com Thu Nov 20 10:34:18 1997 Received: from smtp2.interramp.com for tf004873@psinet.com by www.ccl.net (8.8.3/950822.1) id JAA15742; Thu, 20 Nov 1997 09:45:39 -0500 (EST) From: Received: from psinet.com by smtp2.interramp.com (8.8.5/SMI-5.4-PSI) id JAA19304; Thu, 20 Nov 1997 09:45:27 -0500 (EST) Date: Thu, 20 Nov 1997 09:45:27 -0500 (EST) Message-Id: <199711201445.JAA19304@smtp2.interramp.com> To: chemistry@www.ccl.net Subject: Polymer Scientist Needed I queried the Boolean expression "polymer AND synthesis AND protein" in the DMC Million Plus resume database and several Internet search engines. One of the retrieved resumes, postings or pages advertised your email address indicating that you would welcome email inquiries on related subjects. Hence I am writing to ask for your assistance. I am looking for an Associate Scientist to perform synthesis on biodegradable polymers. Someone with 1+ years experience at a pharmaceutical or bio-tech company possessing a B.S. or M.S. Degree in Chemistry, Chemical Engineering, Medical Sciences or related area. We are a leading biotech firm with research facilities in Baltimore, Maryland and can provide excellent benefits (health insurance, dental, and vision plan, stock options, bonus program, paid vacation and more). A high impact, high profile position with excellent opportunity for advancement. If you know anyone that might be interested please contact: Scott Shanes Voice: 609-584-8733 Ext. 218 Fax: 609-584-9575 OUR ANTI-SPAM POLICY We DO NOT send unsolicited email. 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We will cease mailings and remove your resume for the Diedre Moire Million Plus resume database. Please note that over seventy-five Fortune 500 Corporations and many more small and medium companies tap that database when hiring. Removal of your resume may, in many instances, eliminate your access to jobs at those companies. GENERAL DRAW SOLICITATION We DO NOT support general draw solicitation. General draw is a technique used to "troll" for potential prospects by sending mass quantities of announcements to groups of people in the hopes that some might respond with a general interest. We only announce specific job openings that must be filled immediately and endeavor to contact only those individuals who indicated interest in the related area and made their email addresses available via public posting or resume submission. FORWARDING Sometimes, people we did not send to receive our mail. This occurs when the originally targeted recipient forwards the email we send to a friend or acquaintance. Such forwarding is not under our control. WHO DO WE WORK FOR You may notice the response name and address listed above does not belong to Diedre Moire Corporation, Inc. but some other company, firm or organization. In such cases, Diedre Moire selected your address and mailed to you, but our client requested that referrals, inquiries and candidate applications be made via direct contact to their offices. From robert@pauli.utmb.edu Thu Nov 20 12:34:22 1997 Received: from nmr.utmb.edu for robert@pauli.utmb.edu by www.ccl.net (8.8.3/950822.1) id MAA16345; Thu, 20 Nov 1997 12:08:43 -0500 (EST) Received: from pauli.utmb.edu by nmr.utmb.edu via SMTP (931110.SGI/930416.SGI.AUTO) for CHEMISTRY@www.ccl.net id AA27627; Thu, 20 Nov 97 11:10:28 -0600 Received: (from robert@localhost) by pauli.utmb.edu (950413.SUN.8.6.12/950213.SUN.AUTOCF) id LAA11155; Thu, 20 Nov 1997 11:09:08 -0600 From: "Robert Fraczkiewicz" Message-Id: <9711201109.ZM11154@pauli.utmb.edu> Date: Thu, 20 Nov 1997 11:09:08 -0600 In-Reply-To: Dan Strahs "CCL:visualizing normal modes?" (Nov 18, 1:22pm) References: X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: Dan Strahs , CHEMISTRY@www.ccl.net Subject: Re: CCL:visualizing normal modes? Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dan, > I'm trying to visualize some the normal mode eigenvectors for systems I've > been working with. > > I have a number of options, but none really satisfy me. > You don't have to draw eigenvectors by hand. Program DT2 in the RAMVIB package produces an output in the XYZ format that contains entire set of normal modes with the ACTUAL (i.e., as they come from NCA calculations) eigenvectors. This output is directly readable by, e.g., free molecular graphics program XMol 1.3.1 from Minnesota Suprcomputing Center. Just make sure that the option "Display-Vectors" is set. RAMVIB is available free of charge from CCL archives: ftp://www.ccl.net/pub/chemistry/software/SGI/ramvib/ > > Is there some package (preferably free) which will: > > 1) Display atoms and eigenvectors in a 3-D, rotatable reference > frame; > 2) Allow me to import the entire calculated set of normal modes > and visualize them individually without progressive reloads; > > 3) Generate some form of output (i.e. Postscript) > > Thanks for any help that can be offered in this regard. > > Dan Strahs, Chemistry Dept., NYU XMol can do all of this. In addition, program ANIM from RAMVIB uses DT2 output to generate normal mode animations (30 frames) in XYZ format also readable by XMol. Use option "Extras-Animate" to display the movie. Hope that helps, Robert Fraczkiewicz University of Texas Medical Branch Galveston, TX 77555 From akutatel@du.edu Mon Nov 24 15:37:08 1997 Received: from odin.cair.du.edu for akutatel@du.edu by www.ccl.net (8.8.3/950822.1) id OAA07072; Mon, 24 Nov 1997 14:49:03 -0500 (EST) Received: by odin.cair.du.edu id AA19396; Mon, 24 Nov 1997 12:46:13 -0700 From: "Andrei Kutateladze" To: "CompChemList" Cc: Subject: CCL: g94 LS coupling Date: Mon, 24 Nov 1997 12:39:07 -0700 Message-Id: <01bcf910$a0c095a0$16b0fd82@kizh.biochem.du.edu> Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-Msmail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.71.1712.3 X-Mimeole: Produced By Microsoft MimeOLE V4.71.1712.3 Malisa, You will have to make some minor changes in link 319 and recompile it in order to compute soc integrals for heavy elements. The effective charges for many elements are published in a JPC (1995,12764) paper by the Gordon's group. The use of these charges with Robb's state averaged MCSCF, however, is not documented (at least, I am not aware of this). Since Gordon's charges were optimized for frozen core MCSCF/3-21g* it is conceivable that there might be a problem, although personally I do not believe so. (The charges which are included in G94 are from an older (1992) Gordon's paper). You can certainly use Gamess for your computations, as it allows you to explicitly specify the effective charges in your input file. Hope this is of help Andrei Kutateladze Assistant Professor of Chemistry and Biochemistry University of Denver tel (303) 871-2995 fax (303) 871-2254 From charwel@chrs1.chem.lsu.edu Mon Nov 24 16:37:14 1997 Received: from chrs1.chem.lsu.edu for charwel@chrs1.chem.lsu.edu by www.ccl.net (8.8.3/950822.1) id QAA07489; Mon, 24 Nov 1997 16:21:42 -0500 (EST) Received: by chrs1.chem.lsu.edu (AIX 4.1/UCB 5.64/4.03) id AA36330; Mon, 24 Nov 1997 15:26:14 -0600 Date: Mon, 24 Nov 1997 15:26:14 -0600 (CST) From: Chris Harwell To: ccl Subject: Chemistry on beowulf systems? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII hello, Are there any chemists out there who are using a beowulf cluster of pcs type of system for computing? We are trying to gather some information about software success stories and hardware choices for chemistry applications. Has anyone used gamess, gaussian, or Wien FLAPW on such a system? What hardware choices did you make (processor. motherboard, mem, hard disk, ethernet/fast/atm)? What compiler did you use (gcc f2c, g77)? What OS/Distribution did you use (linux/ redhat or debian?) Any hindsight tempered suggestions to someone considering building such a system? Chris Harwell charwel@chrs1.chem.lsu.edu Chemistry Louisiana State University "Everything positive originates in a positive attitude from someone" :> From chem8@york.ac.uk Mon Nov 24 16:41:11 1997 Received: from pump2.york.ac.uk for chem8@york.ac.uk by www.ccl.net (8.8.3/950822.1) id PAA07280; Mon, 24 Nov 1997 15:36:06 -0500 (EST) Received: from ebor.york.ac.uk (chem8@ebor.york.ac.uk [144.32.129.242]) by pump2.york.ac.uk (8.8.7/8.8.7) with SMTP id UAA24218; Mon, 24 Nov 1997 20:35:17 GMT Date: Mon, 24 Nov 1997 20:35:16 +0000 (GMT) From: John Waite To: Isabel Rozas cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:Basis sets for Sn In-Reply-To: <904*rozas@pinar1.csic.es> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Try the below Isabel. CONTRACTED GTO BASIS FOR Sn STATE: 3P J.WAITE, THE NATIONAL HELLENIC RESEARCH FOUNDATION, ORGANIC CHEMISTRY INSTITUTE, VAS. KONSTANTINOU 48, ATHENS 116-35, GREECE EXPONENTS CONTRACTION COEFFICIENTS S 9 1.0 4.142518414956335D+06 4.914431009415644D-05 6.213291200686644D+05 3.583394001319665D-04 1.421969604620625D+05 2.028952948068900D-03 4.046779700708936D+04 7.524913117315141D-03 1.324973036511741D+04 3.062052366445234D-02 4.806353955774725D+03 7.578488823698701D-02 1.886488717519995D+03 2.343446419619856D-01 7.870073426841410D+02 2.918185230956454D-01 3.440501376507852D+02 4.859816849353728D-01 S 3 1.0 1.541600913220219D+02 -2.781200369991019D-01 6.885453832868097D+01 8.765113933162078D-01 3.183917689497430D+01 3.717163535010151D-01 S 2 1.0 1.210302581710237D+01 1.782503037727801D-01 6.063302228320892D+00 8.341779452261029D-01 S 2 1.0 2.108442407016657D+00 5.090945108670388D-01 9.552945481641465D-01 5.191163687714497D-01 S 2 1.0 1.871317213379940D-01 5.225198765831604D-01 7.209598650018188D-02 5.176982548139625D-01 P 9 1.0 1.200928279101663D+04 9.083195020618228D-04 2.847401888034788D+03 7.755886056457762D-03 9.225290291263347D+02 4.060017207253743D-02 3.502002078849687D+02 1.456724793935791D-01 1.462800691615663D+02 3.397298858349669D-01 6.493827977634784D+01 4.277107016580198D-01 2.968341691740027D+01 1.998060729869509D-01 1.340216559878947D+01 1.765829919542281D-02 6.258288335148135D+00 9.788849511444261D-04 P 3 1.0 2.441768021116800D+00 1.355607482000619D+00 9.830926884984949D-01 -5.681339707937948D-01 2.268755076281387D-01 1.883834408350293D-01 P 1 1.0 7.214945990030488D-02 9.999999999999998D-01 D 5 1.0 3.089734253231580D+02 3.171196242053371D-03 9.149345489299923D+01 -4.043217461811148D-02 3.360063771172553D+01 1.025588528405381D+00 1.327347896060698D+01 0.000000000000000D+00 5.358999527744696D+00 0.000000000000000D+00 D 2 1.0 1.960131229313790D+00 1.183460991889285D+00 6.416256020828989D-01 -3.957316612951171D-01 ENERG= -0.5757661432431780D+04, VIR= -0.19617507D+01, P.E.=-.1174430781D+05, K.E.=0.5986646376D+04, MP2 optimised. F 1 1.0 1.872671004165476D+00 1.0 Dr. John Waite, e-mail: chem8@york.ac.uk * or The National Hellenic Research Foundation,* john@john1.eie.gr Organic and Pharaceutical Chemistry Institute, phone: Vas. Konstantinou 48, phone: ++30-1-7247913(secrtry. Mary) Athens 116-35, fax: ++30-1-7247913 Greece or NCRS "Democritos", phone: ++30-1-6513112-5 X219 * c/o Dr. G.Kordas, e-mail john@john.nrcps.ariadne-t.gr Material Science Institute, Aghia Paraskevi, Attikis, Athens 153-10, Greece On Mon, 24 Nov 1997, Isabel Rozas wrote: > Hi there! > I am looking for basis sets for Sn. I found the STO-3G and > the 3-21G basis sets but I would need something a little > bigger. > Does anybody know where I can get them? or Does anybody > have them available somewhere? > Thanks in advance, > > Isabel Rozas > > ----------------------------------------------------------------------- > Isabel Rozas ROZAS@PINAR1.CSIC.ES > Instituto de Quimica Medica (C.S.I.C.) Phone: 34-1-562 2900 > c/ Juan de la Cierva 3 Fax: 34-1-564 4853 > 28003-Madrid (Spain) > ----------------------------------------------------------------------- > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: rozas@pinar1.csic.es > -- Original Sender From: Address: rozas@pinar1.csic.es > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > From lutz.ackermann@wanadoo.fr Mon Nov 24 17:37:07 1997 Received: from smtp1.wanadoo.fr for lutz.ackermann@wanadoo.fr by www.ccl.net (8.8.3/950822.1) id RAA07764; Mon, 24 Nov 1997 17:33:39 -0500 (EST) Received: from tamaya.wanadoo.fr (tamaya.wanadoo.fr [193.252.19.31]) by smtp1.wanadoo.fr (8.7.5/[France Telecom Interactive]) with ESMTP id XAA07671 for ; Mon, 24 Nov 1997 23:33:32 +0100 (MET) Received: from kip-12.abo.wanadoo.fr [193.252.17.12] by tamaya.wanadoo.fr for Paris Mon, 24 Nov 1997 23:34:55 +0100 (MET) Message-ID: <347A7F1E.17B5@wanadoo.fr> Date: Mon, 24 Nov 1997 23:32:46 -0800 From: "Dr. Lutz Ackermann" X-Mailer: Mozilla 2.02E [fr]-NAVIGATEU (Win16; I) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: CERIUS liquid phase heat capacity calcs Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Netters, I would like to draw on your experience concerning liquid simulation. I have spent the last three month experimenting (I am a novice in the field of MM/MD simulations), trying to solve a problem, but am am not yet satisfied. I am trying to reproduce isobaric heat capacity (Cp) data of single component fluid phase systems (eg. liquid H2SO4), using the MSI CERIUS2_3.0 (OFF) software. MD runs (NPT ensemble) of typically 50ps(equillibration)+120ps(observation) invariably produce Cp values, that are higher than the experimental ones (in general by 30 to 50 percent, in some cases ut to a factor of 3!). This is true for: - more or less complex molecules (3 to 10 atoms) - different force fields - different temperatures - ensembles of different sizes (up to 500 molecules in the unit cell) At the same time, other properties like the density are calculated to a satisfactory degree of accuracy (only a few percent difference to experimental values). Maybe I am expecting to much, but the fact that CERIUS offers the possibility of Cp calculations lead me to believe, that this is actually possible (yielding reliable data, I mean). Are there any experts around, who have managed to calculate realistic heat capacities of liquids (using CERIUS)? Or are there principal reasons, why this doesn't work? Or can you think of some silly mistake I may have made? Maybe you are aware of any publications, that report the successful use of CERIUS in the calculation of the Cp of liquids (although I was told by MSI support that such publications do not exist, as "this is a tricky area"...)? Any other helpful information? Thanks a lot, Lutz Ackermann (101,21869@germany.net / lutz@ri.ac.uk) From glossman@overnet.com.ar Mon Nov 24 19:37:10 1997 Received: from carpincho.overnet.com.ar for glossman@overnet.com.ar by www.ccl.net (8.8.3/950822.1) id SAA08174; Mon, 24 Nov 1997 18:55:13 -0500 (EST) Received: from nppp184.overnet.com.ar (nppp184.overnet.com.ar [200.16.164.197]) by carpincho.overnet.com.ar (8.8.8/8.8.5) with SMTP id UAA06826 for ; Mon, 24 Nov 1997 20:56:31 -0300 Message-Id: <3.0.1.16.19971124204913.1ce78168@pop.overnet.com.ar> X-Sender: dfa953uo@pop.overnet.com.ar X-Mailer: Windows Eudora Light Version 3.0.1 (16) Date: Mon, 24 Nov 1997 20:49:13 To: chemistry@www.ccl.net From: "Dr. M. Daniel Glossman" Subject: using Molden with NT Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear netters: I am looking for somebody in the net who has been succesfull in using the Molden program in a Windows NT environment. I need some advice. Thanks in advance Daniel Glossman *************************************************************************** Dr. M. Daniel Glossman Universidad Nacional de Lujan e-mail: glossman@overnet.com.ar Departamento de Ciencias Basicas Phone: (+54) 323 - 23171 Casilla de Correo 221 Fax: (+54) 323 - 25795 6700 - Lujan Republica Argentina ****************************************************************************