From chemistry-request@server.ccl.net Sat Nov 9 19:32:17 2002 Received: from cornell.edu ([132.236.56.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAA0WHQ10313 for ; Sat, 9 Nov 2002 19:32:17 -0500 Received: from cornell.edu (beech.lassp.cornell.edu [128.84.241.196]) by cornell.edu (8.9.3/8.9.3) with ESMTP id TAA06903 for ; Sat, 9 Nov 2002 19:32:12 -0500 (EST) Sender: cc236@cornell.edu Message-ID: <3DCDA90D.1F087345@cornell.edu> Date: Sat, 09 Nov 2002 19:32:13 -0500 From: Connie Chang X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.2.19-6.2.1smp i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Using Chkpoint files in Gaussian98W Content-Type: multipart/mixed; boundary="------------CEDE18B3F937A117CE4C2A40" This is a multi-part message in MIME format. --------------CEDE18B3F937A117CE4C2A40 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit --------------CEDE18B3F937A117CE4C2A40 Content-Type: message/rfc822 Content-Transfer-Encoding: 7bit Content-Disposition: inline X-Mozilla-Status2: 00000000 Message-ID: <3DCDA8EC.8498B511@cornell.edu> Date: Sat, 09 Nov 2002 19:31:40 -0500 From: Connie Chang X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.2.19-6.2.1smp i686) X-Accept-Language: en MIME-Version: 1.0 To: jmmckel@attglobal.net Subject: Re: CCL:Questions about SCF convergence again with Gaussian98W and Hyperchem References: <3DCBFEF5.39A4EF95@cornell.edu> <3DCBC53F.40CBC6A1@attglobal.net> <3DCC1398.BFDA7432@cornell.edu> <3DCBE74D.16F034A3@attglobal.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi John -- Thanks again for your suggestion... I have one more question. When I have a new job (the anion case), to read in a previously calculated quantity from a checkpoint file, I need to specify the same checkpoint file in my new job, is that correct? But do I need to put in the same rwf files as well? FOr example, if my first job looked like: %chk=molecule.chk %rwf=test1.rwf,280MW, test2.rwf, 280MW,test3.rwf,-1 title #P UPM3 Opt Freq Test 0 1 Should my second job look like this? %chk=molecule.chk %rwf=test1.rwf,280MW,test2.rwf,280MW,test3.rwf,-1 title #P UPM# Guess=Read Geom=Check Opt=Readfc Freq Test -1 2 Or do the rwf (or checkpoint) files need to be different? Thanks, Connie jmmckel@attglobal.net wrote: > Sorry, > > It should have becone #P UPM3 > > John > > Connie Chang wrote: > > > Hi John -- > > I've ran the calculation on the neutral and then using the optimized positions, I > > ran the anion, but it didn't work. Or are you suggesting that I use the > > checkpoint file for the optimized neutral case? > > > > THanks, > > Connie > > > > jmmckel@attglobal.net wrote: > > > > > Connie, > > > > > > Another approach for Gaussian... Optimize the neutral, closed shell molecule, > > > and then using those results, run the doublet anion.... > > > > > > John McKelvey > > > > > > Connie Chang wrote: > > > > > > > Hi everyone -- > > > > > > > > thank you for all your good suggestions... > > > > > > > > I'm still having trouble getting an optimization and frequency > > > > calculation to work for a charged molecule with 120 atoms. I've tried > > > > with both Hyperchem and Gaussian98W using the PM3 method. And I've > > > > tried some fo the suggestions given by listmembers such as increasing > > > > the maximum number of iterations to 500, setting scf=sleazy, setting > > > > scf=qc, etc... I still get the UNABLE TO ACHIEVE SELF CONSISTENCE error > > > > after (at most) one optimization step. So the energy will converge > > > > once, it moves the atoms by a little bit for the optimization and the > > > > energy fails to converge. > > > > > > > > I have the same problem with hyperchem. Hyperchem does the neutral case > > > > just fine, but as soon as I add a charge of -1 and a multiplicity of 2, > > > > the energy does not even get close to something reasonable (it's large > > > > and positive). > > > > > > > > Does anyone have any further suggestions on what I can do to get either > > > > of the programs to work? Hyperchem does work for a smaller molecule > > > > (~70 atoms), but Gaussian does not. Does the size of the molecule make > > > > it more difficult for these programs and methods to find the minimum > > > > energy? I tried a charged water molecule in Gaussian and it worked > > > > fine.... > > > > > > > > thanks. > > > > Connie > > > > > > > > -= This is automatically added to each message by mailing script =- > > > > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > > > > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net --------------CEDE18B3F937A117CE4C2A40-- From chemistry-request@server.ccl.net Sat Nov 9 07:07:26 2002 Received: from mailrelay.tugraz.at ([129.27.3.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA9C7PQ31830 for ; Sat, 9 Nov 2002 07:07:25 -0500 Received: from novzid.tu-graz.ac.at (novzid.tu-graz.ac.at [129.27.3.150]) by mailrelay.tugraz.at (8.12.6/8.12.6) with ESMTP id gA9C7NW4005352; Sat, 9 Nov 2002 13:07:23 +0100 (MET) Received: from ZID/SpoolDir by novzid.tu-graz.ac.at (Mercury 1.48); 9 Nov 02 13:07:23 +0100 Received: from SpoolDir by ZID (Mercury 1.48); 9 Nov 02 13:07:13 +0100 Received: from TweedleDum.local. (129.27.240.80) by novzid.tu-graz.ac.at (Mercury 1.48) with ESMTP; 9 Nov 02 13:07:06 +0100 Date: Sat, 9 Nov 2002 13:07:12 +0100 Subject: xhCML browser in JavaScript/HTML Content-Type: text/plain; charset=US-ASCII; format=flowed Mime-Version: 1.0 (Apple Message framework v540) Cc: Alk Dransfeld To: chemistry@ccl.net From: Alk Dransfeld Content-Transfer-Encoding: 7bit Message-Id: X-Mailer: Apple Mail (2.540) X-Virus-Scanned: by amavisd-milter (http://amavis.org/) What do chemists want ? Collect data, conclude and write an article WITHOUT having to retype all the data. Some MacOS and Microsoft based publishing tools have recently included the features of generating diagrams in an article/report > from raw-data in spreadsheets. Unfortunately - or naturally - when data and layout are separated once, these programs can not reunite facts and visualisation. With the presented "Data-In-Article" (DinA) approach incorporating raw data in a fluently readable document is possible (like including images in HTML). DinA, my first implementation of a CML browser at http://www.cis.tugraz.at/aoc/sharc/dina/ is written in JavaScript/HTML and is therefore platform independent. The read and retrieve functions of DinA are general XML tools[1] while the chemical features are xhCML and xhCMLpath based. xhCml is an eXtensible Hierarchical Chemical MarkupLanguage which complies with the rules of XML xhCmlPath is an Xpath like pointer, which allows to address data in a set of xhCML data. Please visit the demo site http://www.cis.tugraz.at/aoc/sharc/dina/ and see what DinA can do for you or simply play with chemical markup or be inspired to think about CML. Thanx - alk +++ In the following you are guided through the demo, the features of xhCML and DinA are pointed out, and obstacles and perspectives discussed. # For a quick start press the "[re]build article" button and see how the values from the xhCML documentation of two measurements are inserted into the 'article' (in HTML). For an example of the xhCML2myvalue function press the "demo 1" and then the "a" button on its right. Try to follow the xhCMLpath to find the requested value in the xhCML documentation and press the "show value of xhCMLpath" button to see whether your guess was right. # Why xhCml ? xhCml is - eXtensible Hierarchical = when experts require more detailed descriptions they can extend the language in their context (branch in hierarchy) WITHOUT need of having everyone else change their documents [note, this is NOT the same as using various namespaces] - Chemical ... oh, since it's for chemistry - MarkupLanguage ... a child of XML The hierarchy is essential to use reliable pointers (see Xpath). The hierarchy reflects chemical understanding [NOT Java-object structure]. The hierarchy starts with (CML is root, first branches are): MEASURED = all you can detect MODELED = all you can simulate CONJUNCTION = connecting statements, which lead to abstract knowledge in the end f.i. define the rms-error of a method by linking a set of related measured and modeled values For differentiation between similar branches in the hierarchy identifier attributes similar to the SHARCid are required (f.i. ). Effective retrieval, use in publishing respectively, is based on such identifiers. # What's DinA The demo screen comprises three frames (input,navigation,article): A. (top frame) the input fields for documentation of chemistry "xhCML" and the retrieval request "xhCMLpath". With the button "show value of xhCMLpath" you can see the value/string the retrieval lead by xhCMLpath returns. B. (middle) the button to generate the article considering the xhCML { if you change the xhCML the 'article' changes on your click } With the buttons on the right you can fill example xhCML_s and related example xhCMLpath_s in the input fields above and use them. C. (bottom frame) the fluently readable document generated with JavaScript/HTML from xhCML. Additionally the hierarchy/tree of the xhCML nodes is shown. D.rawback: since the XML parser used is fast + free[1] but ONLY a parser invalidity of the xhCML, XML respectively, is only notified with an error message starting with "ERROR may be due to nested tags - sorry. # Obstacles and Perspective Since HTML is a slang dialect of XML embedding the xhCml directly in the HTML is not save nowadays. Embedding with would be the ultimate way to do TMHO - in the future. For now in the frameset the data is in the left input field of the top frameset and the HTML linking in these data is in the bottom frame. This construct offers the possibility to change the demo data and on the fly see how the 'article' changes. The JavaScript 'program' does not only allow to include a value or string from the data set but also has derived functions, f.i. the difference of two values. Note that a computed chemical shift can also be described as a sum of an experimental and a calculated values for a reference molecule together with the calcuated shielding of the 'resonant' nucleus in the target molecule (the future of NMR-SHARC). [1] JavaScript package Xparse.91 Feb 21 1998 , Jeremie from http://www.jeremie.com Looking forward to more discussion+development in this field -A.Dransfeld From chemistry-request@server.ccl.net Sun Nov 10 17:40:51 2002 Received: from dux.ru ([193.125.210.65]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAAMepQ06945 for ; Sun, 10 Nov 2002 17:40:51 -0500 Received: from dux.ru (localhost [127.0.0.1]) by dux.ru (8.12.6/8.12.6) with ESMTP id gAAMkhZs005485 for ; Mon, 11 Nov 2002 01:46:53 +0300 (MSK) (envelope-from dima@xenon.spb.ru) Received: (from uucp@localhost) by dux.ru (8.12.6/8.12.1/Submit) with UUCP id gAAMkdAO005482 for chemistry@ccl.net; Mon, 11 Nov 2002 01:46:39 +0300 (MSK) (envelope-from dima@xenon.spb.ru) Received: from goblin (goblin [192.168.3.2]) by shadow (8.9.3/8.9.3/Debian 8.9.3-21) with SMTP id BAA21809 for ; Mon, 11 Nov 2002 01:32:29 +0300 Message-ID: <00ca01c28909$0f29bde0$0203a8c0@goblin> From: "Dmitry Rozmanov" To: "CCL" Subject: Molecular Dynamics for cations in water Date: Mon, 11 Nov 2002 01:32:32 +0300 MIME-Version: 1.0 Content-Type: text/plain; charset="koi8-r" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 Hi. I am looking for freeware MD simulation software that is sutable for modelling metal cations in water solutions. I am planning to use tree body potentials as well, so there should be a possibility to use them. Is there any software that one can recommend to me? Thank you in advance. Regards. ---Dmitry. From chemistry-request@server.ccl.net Sun Nov 10 09:49:58 2002 Received: from sina.com ([202.108.35.238]) by server.ccl.net (8.11.6/8.11.0) with SMTP id gAAEnuQ32364 for ; Sun, 10 Nov 2002 09:49:56 -0500 Received: (qmail 7814 invoked by uid 99); 10 Nov 2002 14:45:11 -0000 Message-ID: <20021110144511.7813.qmail@sina.com> From: chenghuiqc To: chemistry@ccl.net Subject: change the PCM atom radii in Gaussian98 MIME-Version: 1.0 Date: Sun, 10 Nov 2002 22:45:11 +0800 X-Mailer: SinaMail 3.0Beta (FireToad) X-Priority: 3 Dear Sir, I am using the PCM model in Gaussian98 to study some solvent effects in a reaction, but I find that I can not use "alpha=1.3" to change the radii of the atom as the instruction of the gaussian help.Who can tell me how I can change the radii? Thank you. chenhui Chem Dept Nanjing Univ P.R.China ______________________________________ =================================================================== 免费试用新浪15M收费邮箱 赶紧行动！ (http://vip.sina.com/sol_mail/promotion/pro_men.html) 新浪二手市场：一元投入，十分惊喜，百分满意 (http://classad.sina.com.cn/2shou/) 数万张手机图片数万首短信铃声任你挑选，每天都有更新 (http://sms.sina.com.cn/cgi-bin/sms/smspic.cgi) From chemistry-request@server.ccl.net Sun Nov 10 20:06:58 2002 Received: from yakko.cimav.edu.mx ([148.223.46.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAB16vQ09447 for ; Sun, 10 Nov 2002 20:06:57 -0500 Received: from prima ([148.223.46.123]) by yakko.cimav.edu.mx (8.11.6/8.11.2) with SMTP id gAB1wt232217 for ; Sun, 10 Nov 2002 18:58:55 -0700 Message-ID: <009f01c2891f$135f4f40$ae00000a@cimav.edu.mx> From: "Dr. Daniel Glossman-Mitnik" To: Subject: a question about molecular computational chemistry Date: Sun, 10 Nov 2002 18:10:06 -0700 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_009C_01C288E4.66389360" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 Disposition-Notification-To: "Dr. Daniel Glossman-Mitnik" X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 This is a multi-part message in MIME format. ------=_NextPart_000_009C_01C288E4.66389360 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear netters: I would like to know your opinion about the following subject: * In your opinion, has any meaning (and sense) to speak about Molecular Computational Chemistry or=20 Computational Molecular Chemistry ? * If so, which would be and which would be NOT the subjects of study in each field ? Thanks in advance. Dr. Daniel Glossman-Mitnik ********************************************************************** Dr. Daniel Glossman-Mitnik CIMAV - Centro de Investigacion en Materiales Avanzados LAQUICOM - Laboratorio de Quimica Computacional Miguel de Cervantes 120 - Complejo Industrial Chihuahua Chihuahua, Chih. 31109 - Mexico Tel: (52) 614 4391151 FAX: (52) 614 4391112 E-mail: daniel.glossman@cimav.edu.mx glossman@hotmail.com dglossman@yahoo.com ********************************************************************** ------=_NextPart_000_009C_01C288E4.66389360 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
 
Dear netters:
 
I would like to know your = opinion about=20 the following subject:
 
* In your opinion, has any = meaning (and=20 sense) to speak about
 
   Molecular = Computational=20 Chemistry
 
or
 
 Computational Molecular = Chemistry   ?
 
 
* If so, which would be and = which would=20 be NOT the subjects of study
    in each = field=20 ?
 
 
Thanks in = advance.
 
 
          &nbs= p;            = ;            =       =20 Dr. Daniel Glossman-Mitnik
 
****************************************************************= ******
Dr.=20 Daniel Glossman-Mitnik
CIMAV - Centro de Investigacion en Materiales=20 Avanzados
LAQUICOM - Laboratorio de Quimica Computacional
Miguel = de=20 Cervantes 120 - Complejo Industrial Chihuahua
Chihuahua, Chih. = 31109 =20 -  Mexico
Tel: (52) 614 4391151      = FAX: (52)=20 614 4391112
E-mail: daniel.glossman@cimav.edu.mx=
           = ;=20 glossman@hotmail.com
 &n= bsp;         =20 dglossman@yahoo.com
**********= ************************************************************
= ------=_NextPart_000_009C_01C288E4.66389360--