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From owner-chemistry@ccl.net Thu Dec 21 02:27:00 2006 From: "Jan Labanowski janl..speakeasy.net" To: CCL Subject: CCL: Happy Holidays and New Years Message-Id: <-33289-061220223255-1234-8CX0RGQvf8cy6p3//4wn+w*_*server.ccl.net> X-Original-From: "Jan Labanowski" Content-Type: multipart/mixed; boundary="--=_vm_0011_W842542528_2773_1166684796" Date: Thu, 21 Dec 2006 07:06:36 +0000 MIME-Version: 1.0 Sent to CCL by: "Jan Labanowski" [janl-x-speakeasy.net] ----=_vm_0011_W842542528_2773_1166684796 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Dear CCL, Now that some of you had your holidays, and some of you will have them in a few days it may be a right time to be religiously and politically correct to wish everyone good time. In any case, there is a New Year which most of us look forward with hope and expectations. Also, it is a good time to write this message, since judging from the number of automatic "vacation" responses that my bouncebox collects, not many of you will waste time to read it. But anyhow, for the record, it is here, and you can find it in CCL archives... As I am at this... If you get in the library the copy of Academe, the magazine of American Association of University Professors (http://www.aaup.org), there will be a short piece in Jan/Feb issue about CCL: "Mixing the Media on CCL.NET" (they made a title -- it was supposed to be "non-technical") as a part of larger feature "Free Speech, Quality Control, and Flame Wars". I am waiting for the issue myself to check how much I disagree with other contributors (I honestly do not know...) and if I can recognize it after editing and adopting... At least we have been recognized as a lasting virtual community even though the Computational Chemistry is a discipline of the future and will always be this... So... All the best to all of you for staying with CCL for short of long. I will try to be optimistic (this is Holiday Greetings, for God's (G-d's?) sake...), so please do not confuse it with unfounded expectations. So let us all hope that "There will be Peace on Earth..." and economy will grow (everywhere...) and make us prosperous, and that there will be ample research resources that will be given to those who should get them without the need of sending boxes of paper (or submitting gigabytes to FastLanes), and that we will all be breathing better air, eat organic food (but without E. coli) and have nice weather without a danger of melanoma or heat exhaustion, while the hurricane, tornadoe, cyclone and monsoon seasons will be mild and actually nice. And of course, winter will be like the old times (of course, those guys who are upside-down can substitute summer here), and the spring will be blooming, and we will be flying for our dream vacations with the whole tube of toothpaste and two bottles of soda rather than half of this amount, as prescribed by law. So... Let us drink to it on the New Year's Eve and dance the whole night in the streets without being checked with metal detectors and watched carefully with the night-vision equipment that will automatically scan our facial expression and take biometric measurements. And let us also wish that our Holiday/New Year's Greetings, especially the international ones, are not confused by busy computers with coded messages and our presents are safely and efficiently scanned and that they do not need to be checked in the lab and arrive to the destination late and in atomized state. So again... All the best... Have fun... God's speed... And enjoy. I am attaching an HTML file with my traditional Christmas (sorry... Holiday) Tree with the list of popular orthographic and grammar mistakes in many languages of the world. Jan The Proud Manager of the Renowned CCL World Virtual Community Forum (How's this for a title?...) ----=_vm_0011_W842542528_2773_1166684796 Content-Type: text/html; name="choinka2006.html" Content-Disposition: attachment; filename="choinka2006.html" Content-Transfer-Encoding: 7bit choinka

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                  X_ 2006 X                                                   
                "BOAS FESTAS"                                                 
                "JOYEUX  NOEL"            \ /                      *          
               "VESELE VANOCE"           --O--                    XXX         
              "MELE KALIKIMAKE"           / \                   "HOME"        
             "NODLAG SONA DHUIT"                               "PEACE."       
            "BLWYDDYN NEWYDD DDA"                            "BON NADAL."     
                  "GOD__JUL"                               "BOLDOG UJ EVET"   
                 "BUON--ANNO"        \ /                  "CHANUKAH SAMEACH"  
   \ /          "FELIZ**NATAL"      --O--                     "DOSIEGO!"      
  --O--       "FELIZ..NAVIDAD."      / \                   "HAPPY HANUKKAH"   
   / \       "KALA CHRISTOUGENA"                          "PARI  ARTSAGOURT"  
            "VROLIJK  KERSTFEEST"                        "KELLEMES UNNEPEKET" 
           "FROEHLICHE WEIHNACHTEN"                    "NAYA VARSH SHUBH HO"  
          "BUON  NATALE-GODT NYTAR"                   "ATHBHLIAIN FAOI MHAISE 
         "HUAN YING SHENG TAN CHIEH"                "IYI YILLAR-HYVAEAE LOMAA 
        "WESOLYCH SWIAT-SRETAN BOZIC"       \ /             "NA  ZDOROVE"     
       "MOADIM LESIMHA-LINKSMU KALEDU"     --O--          "MERRY CHRISTMAS"   
      "HAUSKAA JOULDA-AID SAID MOUBARK|     / \          "FELICHAN JARFINON"  
           "'N  PRETTIG  KERSTMIS"    O                 "O*SHUB NAYA BARAS*O" 
          "ONNELLISTA UUTTA VUOTTA"  (*) !            "INPAKARAMAANA VIDUMURAI
         "Z ROZHDESTVOM  KHRYSTOVYM"    =+=          "STASTNY NOVY ROK-CHEERS*
        "NADOLIG LLAWEN-GOTT NYTTSAR"    !          "CHING CHI SHEN TAN-o_o_o_
      "CRACIUN FERICIT-GOJAN KRISTNASKON"                  ***  **!!          
      "S  NOVYM  GODOM-FELIZ ANO NUEVO"          .-'-.  mmmmmm  !!!!          
     "GLEDILEG JOL-NOELINIZ KUTLU OLSUM"      .-' .-. '-.!  !   xxxx          
    "EEN GELUKKIG NIEUWJAAR-SRETAN BOSIC"  .-' .-'   '-. '-.!    .            
   "KRIHSTLINDJA GEZUAR-KALA CHRISTOUGENA"  .-'         '-. '-.               
  "SELAMAT HARI NATAL - LAIMINGU NAUJU METU"'               '-. '-.           
       "SARBATORI FERICITE-BUON  ANNO"   !   ___________     !-..!-           
      "ZORIONEKO GABON-HRISTOS SE RODI"  !   !__o_!__!__!    !                
     "BOLDOG KARACSONNY- VESELE  VANOCE" !   !_ooo!__###__!    !                
    "MERRY CHRISTMAS**JOY**HAPPY NEW YEAR"   !ooooo__#__!    !      (\_/)-=)) 
   "ROOMSAID JOULU PUHI -KUNG HO SHENG TEN"     .            !     =('.')=//  
  "FELICES PASUAS-EIN GLUCKICHES  NEUEJAHR*.-.-' -.._________!     ( ~~~ )/   
"PRIECIGUS ZIEMAS SVETKUS  SARBATORI VESLLE"            '-.-''-..  `w---w`    
"BONNE ANNEE-BLWYDDYN NEWYDD DDA*FELIZ NATAL"                     '-....      
SHENORAVOR SOORP TSENOONT,SHENORAVOR NOR DARI"                                
EID MUBARAK -o- MALIGAYANG PASKO -o- GEZEELLIGE"                              
KERSTMIS -|- CHRISTUJUMNA RUKSHUMMA -|- PIVDLUANA"                            
JODLUME UKIOTARME-LO ~|~ HAUOLI MAKAHIKI HOU ~|~ "                            
CHUC MUNG NGAY TROI SINH - CHUC MUNG NAM MOI--*(O)*"                          
HAPPY KWANZAA ~*~ NODLAIG MHAITH CHUGNOT*X*X*(*)*X*X"
SRECNA NOVA GODINA -o- SUNGTAN CHUKHA * MERII KURISUMASU
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----=_vm_0011_W842542528_2773_1166684796-- From owner-chemistry@ccl.net Thu Dec 21 11:35:00 2006 From: "Jens Spanget-Larsen spanget_+_ruc.dk" To: CCL Subject: CCL: "Experiments" in Quantum Chemistry for Non-chemists? Message-Id: <-33292-061221112309-30591-SlvpKfEwnKb78QfOjvV/1Q:-:server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 21 Dec 2006 16:52:30 +0100 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget**ruc.dk] Dear Ralf, I appreciate your problem. I have attempted to develop lectures and computer demonstrations, illustrating the use of molecular modelling and quantum chemistry, for non-expert audiences (highschool classes (Gymnasium); general public visitors in open-house arrangements; etc). It is not easy. And half-an-hour is a very short time. We have had some success with a demonstration based on molecular vibrations and IR spectroscopy. We start with an introduction to the world of molecules, the very small bodies that chemical substances and most matter are composed of. The molecules can be considered as small mechanical objects that can vibrate with characteristic frequencies, just like musical instruments. But we cannot hear the 'tones' of a molecule because it is so small. However, we can observe them as peaks in an IR spectrum: If the frequency of the radiation matches a molecular frequency, energy can be absorbed and we see a peak in the absorption spectrum. The scene is thus set for animation of molecular vibrations on the computer screen by using suitable quantum chemical procedures (or pre-stored animations), comparison with experimental spectra, identification of 'unknown' compounds, etc. There are many possibilities. But it is hard to carry out this program in less than an hour, particularly if the audience shall have their own time on the computers! Good Luck! Jens >--< ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science (18.1) Fax: +45 4674 3011 Roskilde University Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget===ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ Ralf Tonner Tonner.===.chemie.uni-marburg.de wrote: > Sent to CCL by: Ralf Tonner [Tonner-x-chemie.uni-marburg.de] > Dear CCLers, > > since a few years the "Chemikum" exists at the University of > Marburg (www.chemikum-marburg.de) as a possibility for > pupils, adults and kids to learn to know the experimental > world of chemistry and do some instructive experiments on > their own. > > As a further extension to this project, our group has been > asked to contribute with an "experiment" or interesting > presentation from the computational chemistry side. > > As all of you know, presenting our topics even to chemists > can be a tedious task, so I was searching the web for nice > didactic "experiments" on the computer but unsuccessful up > to know. > > Is anyone aware of a resource where to fetch some ideas or > publicly available presentations/experiments which fulfill > the requirements of being finished in at most half an hour > without any pre-knowledge in quantum chemistry and at best > let non-chemists gain some insight ? > > I would hardly have the time and educational knowledge of > setting up something completely from scratch... > so I am very grateful for any suggestions. > > Thanks for your help > > Ralf. > > From owner-chemistry@ccl.net Thu Dec 21 12:10:00 2006 From: "T-Tsuru_._coral t-tsuru_._coral.dti.ne.jp" To: CCL Subject: CCL:G: Summary) Non-GUI programs Message-Id: <-33293-061221100732-20225-xQ7EbTtdeIdi7SQo6OFY8w===server.ccl.net> X-Original-From: "T-Tsuru%coral" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-2022-jp"; reply-type=original Date: Thu, 21 Dec 2006 23:32:52 +0900 MIME-Version: 1.0 Sent to CCL by: "T-Tsuru ~ coral" [t-tsuru ~ coral.dti.ne.jp] Hello, CCLers. I sent following question last week. It was concerning the "old-style" MO program. ----- Original Message ----- To: "Tsuru, Telkuni " Sent: Saturday, December 16, 2006 10:30 PM Subject: CCL: Non-GUI programs > > I'm looking for non-GUI molecular orbital calculation programs. Resent MO > programs have rich GUI functions. This is not better to me. Because of two > reasons as follows: > 1) I want to check the calculation progress precisely with text-style output. > But GUI forbids it. > 2) I would like to develop the original output editor by Flash-movie. > > Does anyone know such "old-style" available free program ? > I don't care that it is EHMO or ab-initio. > And I don't care that it runs on MS-DOS(my PC is Windows). Here is the summary. *** I'm sorry. I forgot to write that I have Gaussian98W ! *** And I forgot to write the phrase: "non-GUI program which except for G98W." --- 1) from Dr. Jim Kress --- PCGAMESS and WINGAMESS Come to mind immediately, for a Windows PC - and are free. Dalton, PCGAMESS, GAMESS, MOLPRO, MPQC, NWChem, and Orca come to mind for a Linux machine - and are free, except for MOLPRO. Jaguar and ADF can probably be run from the command line too. You probably don't need to use the GUI interface. But these cost big bucks. Jim --- 2) from Dr. J. P. Stewart --- Please consider using MOPAC 7.2 from HTTP://OpenMOPAC.net Jimmy Stewart --- 3) from Dr. Odon Farkas Among the others, Gaussian is also available for Windows and the academic site-wide license seems to be a good deal. Good luck, ---------------------------------------------------- Telkuni Tsuru t-tsuru**coral.dti.ne.jp Bunshi Gijyutu From owner-chemistry@ccl.net Thu Dec 21 12:44:00 2006 From: "=?ISO-8859-1?Q?Nicolas_Ferr=E9?= nicolas.ferre:_:univ-provence.fr" To: CCL Subject: CCL: Statistical relevance of an average property Message-Id: <-33294-061221104926-28263-MVFOKb8Oy3pReD8PnUyFOA*o*server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Nicolas_Ferr=E9?= Content-Type: multipart/mixed; boundary="------------010502060100010604020106" Date: Thu, 21 Dec 2006 16:16:01 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Nicolas_Ferr=E9?= [nicolas.ferre|univ-provence.fr] This is a multi-part message in MIME format. --------------010502060100010604020106 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Dear CCL, I am wondering what is the minimal ratio of structures extracted from a MD trajectory that allows to compute an average property with statistical relevance ? Does it depend on the length of the trajectory ? If the ratio I want to use is not enough, shall I weight the property according to a Boltzmann distribution ? Best regards, -- NF --------------010502060100010604020106 Content-Type: text/x-vcard; charset=utf-8; name="nicolas.ferre.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="nicolas.ferre.vcf" begin:vcard fn;quoted-printable:Nicolas Ferr=C3=A9 n;quoted-printable:Ferr=C3=A9;Nicolas org;quoted-printable:Universit=C3=A9 de Provence;UMR "Chimie, Biologie, Radicaux Libres" adr;quoted-printable:Case 521;;Facult=C3=A9 de Saint-J=C3=A9r=C3=B4me;Marseille Cedex 20;;13397;France email;internet:nicolas.ferre[at]univ-provence.fr title;quoted-printable:Ma=C3=AEtre de Conf=C3=A9rences tel;work:+33 491282733 tel;fax:+33 491288758 tel;cell:+33 615995320 note:Please replace [at] with the right symbol to get my correct electronic mail address x-mozilla-html:FALSE url:http://www.up.univ-mrs.fr/cbrl/lctmm version:2.1 end:vcard --------------010502060100010604020106-- From owner-chemistry@ccl.net Thu Dec 21 15:40:01 2006 From: "Jeff Nauss jnauss|*|accelrys.com" To: CCL Subject: CCL: Statistical relevance of an average property Message-Id: <-33296-061221135317-32150-juJn/F+HYE9BV2QBdRN5zQ,,server.ccl.net> X-Original-From: Jeff Nauss Content-Type: text/plain; charset="US-ASCII" Date: Thu, 21 Dec 2006 10:13:54 -0800 MIME-Version: 1.0 Sent to CCL by: Jeff Nauss [jnauss/./accelrys.com] > Sent to CCL by: =?ISO-8859-1?Q?Nicolas_Ferr=E9?= [nicolas. > ferre|univ-provence.fr] > I am wondering what is the minimal ratio of structures extracted from a > MD trajectory that allows to compute an average property with > statistical relevance ? Does it depend on the length of the trajectory ? > If the ratio I want to use is not enough, shall I weight the property > according to a Boltzmann distribution ? It depends on the timescale of the property that you are measuring. Simple bond and angle vibrations could be properly sampled in a few picoseconds. But conformational transitions require nanosecond runs. I recommend you consider using autocorrelation functions to make a quantitative assessment as to whether you have sampled enough. I'd like to hear other opinions as well. Jeff -- Jeffrey L. Nauss, Ph.D. Lead Training Scientist Accelrys 10188 Telesis Court, Suite 100 San Diego, CA 92121-4779 Phone: +1-858-799-5555 Fax: +1-858-799-5100 http://www.accelrys.com/services/training/