From owner-chemistry@ccl.net Fri May 9 02:44:00 2008 From: "Radhakrishan S radhas78]*[gmail.com" To: CCL Subject: CCL:G: Calculation of thermal conductivity Message-Id: <-36921-080509020151-8044-NTUNpc5PjXoJlHlL7cdmaA^^server.ccl.net> X-Original-From: "Radhakrishan S" Date: Fri, 9 May 2008 02:01:46 -0400 Sent to CCL by: "Radhakrishan S" [radhas78]=[gmail.com] Dear Members, Can anyone suggest me how to calculate thermal condcutivity data of a molecule by quantum chemical calculations. (Preferably from Gaussian Calculations) Thanks in advance Radhakrishnan From owner-chemistry@ccl.net Fri May 9 08:46:01 2008 From: "Rishi Pandey rish.iisc*|*gmail.com" To: CCL Subject: CCL:G: Solute radius for the SCRF calculation Message-Id: <-36922-080509054546-16943-rGpBYstNKShNqp4m6kf/3Q|,|server.ccl.net> X-Original-From: "Rishi Pandey" Date: Fri, 9 May 2008 05:45:40 -0400 Sent to CCL by: "Rishi Pandey" [rish.iisc||gmail.com] Dear all, I want to perform some SFRF calculations using Onsager model(Gaussian 03 program).Calculation requires the solute radius in the gas phase which can be calculated using Volume keyword.I run a Volume job thrice starting from the identical input as well as the job setup(basis set-b3lyp-6311g**).I got three diffrent solute radai.I wonder how can I find out which one is the right one. I will heartly appreciate for anykind of suggestions. Regards Rishi From owner-chemistry@ccl.net Fri May 9 09:21:01 2008 From: "Kamila Morawski kamila.morawski[#]scienomics.com" To: CCL Subject: CCL: Scientifical advances in modeling and simulation technology - Seminar Message-Id: <-36923-080509052245-14848-xwMcvbc3ko8VbWvc/WvZtQ(0)server.ccl.net> X-Original-From: "Kamila Morawski" Date: Fri, 9 May 2008 05:22:31 -0400 Sent to CCL by: "Kamila Morawski" [kamila.morawski^^scienomics.com] Dear Scientists, Scienomics is pleased to invite you to join us at the presentation seminar on Molecular Modeling and Simulations organised with the support of Sun Microsystems and Consejo Superior de Invesigaciones Scientificas (CSIC) held in CSIC Madrid premises on Tuesday May 20th 2008. We are proud to announce the release of a new major version of the Materials and Processing Simulation Platform (MAPS) and during this one day event both unexperienced and experienced modelers are invited to hear presentations and case studies from Scienomics' technology users and scientists, see demonstration of MAPS' new features and participe to an interactive hands on session during which each participant will have the opportunity to approach our technology. Scienomics' integrated materials and processes design and simulation products and services offer competitive advantages to its users, such as access to advanced simulation technologies, shortened product time-to-market, reduced total cost of ownership and more effective asset utilization. - What can you expectfrom this event? Hear presentations from experienced scientists See demonstration of MAPS technology and new features Participate to a hands on session and experience MAPS technolgy Gain insight into Scienomics technology Learn how to improve your R&D processes Interact with participants and present users Learn about Sun Microsystems and Scienomics new partnership - Who should attend? Research Directors R&D Directors Catalysis and Petrochemical Scientists Materials Scientists Polymer Scientists Chemical Development Researchers Analytical Scientists Pharmacists Toxicologists If you wish to receive the agenda ot this event or have more informations, don't hesitate to contact us: kamila.morawski[A]scienomics.com or + 33 1 53 43 91 67 We look forward to welcoming you on May 20th. Best regards, The Scienomics team From owner-chemistry@ccl.net Fri May 9 09:56:01 2008 From: "Lilianna Bryjko lb435|a|st-andrews.ac.uk" To: CCL Subject: CCL: How convert gamess orbitals to molpro orbitals Message-Id: <-36924-080509064041-25689-QbatgS/iXInEYditWubNMw^server.ccl.net> X-Original-From: "Lilianna Bryjko" Date: Fri, 9 May 2008 06:40:37 -0400 Sent to CCL by: "Lilianna Bryjko" [lb435.-.-.st-andrews.ac.uk] I'm looking for informations if there is any way to convert Gamess (US) orbitals to Molpro orbitals. Does maybe Gamess (US) have the option to print Molpro format orbitals. Lilianna Bryjko University of St Andrews From owner-chemistry@ccl.net Fri May 9 10:30:01 2008 From: "Dr. Christian =?utf-8?q?M=C3=BCck-Lichtenfeld?= cml- -uni-muenster.de" To: CCL Subject: CCL: DFT-D using Turbomole Message-Id: <-36925-080507145122-30222-9HGAgNGX9ipmoLHTCIgmKw!A!server.ccl.net> X-Original-From: "Dr. Christian =?utf-8?q?M=C3=BCck-Lichtenfeld?=" Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Date: Wed, 7 May 2008 20:51:06 +0200 MIME-Version: 1.0 Sent to CCL by: "Dr. Christian =?utf-8?q?M=C3=BCck-Lichtenfeld?=" [cml%uni-muenster.de] Hello Jiten, let me as someone who has been involved in the development of DFT-D shortly explain how you can use it in Turbomole (5.10). The keyword $disp allows you to switch on the dispersion correction for the following functionals: b-lyp, b97-d, b3-lyp, tpss, b-p, pbe (for b97-d you should always turn the correction on because the functional parameters have been fitted together with the dispersion correction). Each of the functionals has a specific s6-Parameter that scales the size of the dispersion contribution. The keyword $olddisp activates the older (superseded) version of the 2004 paper (J. Comput. Chem. 25, (2004), 1463). In the current version of Turbomole you can not use other functionals together with the dispersion correction (the program will simply stop). This will probably be changed in the next release. After $disp you may give one single real number for s6 that overrides the published, predefined value for the functional you have chosen. You can also not define C6 or R0 terms for the elements yourself ! These parameters have been obtained from clearly defined formulas (see J. Comput. Chem. 27, (2006), 1787) and are not supposed to be changed. I hope this has cleared some open points. With my best regards, Christian Mueck-Lichtenfeld On Tuesday, 6. May 2008 09:02:51 JITEN SINGH jiten]![postech.ac.kr wrote: > Sent to CCL by: "JITEN SINGH" [jiten]^[postech.ac.kr] > Hi all, > > Grimme's method for the calculation of DFT-D has been found to be > implemented in Turbomole V5.10. However, the manual is not clearly > documented for the usage of in the turbomole manual. I am wondering if > someone provide a step by step instructions to use DFT-D with turbomole. > > I am familiar with rimp2 and ridft > > Your help will be highly appreciated. > > Best wishes, > > Jiten =2D-=20 =2D------------------------------------------------------------------ Dr. Christian M=C3=BCck-Lichtenfeld Westfaelische Wilhelms-Universit=C3=A4t Organisch-Chemisches Institut Corrensstrasse 40 D-48149 M=C3=BCnster, Germany cml%%uni-muenster.de =C2=A0 =C2=A0Tel +49 251 83 33301 =C2=A0 =C2=A0Fax +49 = 251 83 36506 http://www.uni-muenster.de/Chemie/OC/research/grimme/group/cml.html =2D------------------------------------------------------------------ =C2=A0 =C2=A0 =C2=A0 support the progress of Quantum Chemistry with your PC =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 http:= //qah.uni-muenster.de=20 =2D------------------------------------------------------------------ From owner-chemistry@ccl.net Fri May 9 11:10:00 2008 From: "Nicholas Labello label030-.-umn.edu" To: CCL Subject: CCL: How convert gamess orbitals to molpro orbitals Message-Id: <-36926-080509104404-26520-IyYvZceRebjWImuKK6BqgQ\a/server.ccl.net> X-Original-From: Nicholas Labello Content-Type: multipart/alternative; boundary="------------010508030105080306050804" Date: Fri, 09 May 2008 09:43:52 -0500 MIME-Version: 1.0 Sent to CCL by: Nicholas Labello [label030###umn.edu] This is a multi-part message in MIME format. --------------010508030105080306050804 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit I don't know of an option to automatically do this conversion, but the .dat file includes the information you need (make sure you retrieve it from scratch). The $DATA group has the atomic coordinates and basis set and is followed by the $VEC group which contains the molecular orbitals. They are human-readable and nicely formatted; if you're familiar with the Molpro format a Perl or Python script could make quick work of it. *Nicholas Labello Postdoctoral Associate* /Center for Drug Design The University of Minnesota 308 Harvard Street Minneapolis, MN 55455 (612) 626-4429/ Lilianna Bryjko lb435|a|st-andrews.ac.uk wrote: > Sent to CCL by: "Lilianna Bryjko" [lb435.(a).st-andrews.ac.uk] > I'm looking for informations if there is any way to convert Gamess (US) orbitals to Molpro orbitals. Does maybe Gamess (US) have the option to print Molpro format orbitals. > > Lilianna Bryjko > University of St Andrews> > > -- * *// --------------010508030105080306050804 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit I don't know of an option to automatically do this conversion, but the .dat file includes
the information you need (make sure you retrieve it from scratch).  The $DATA group has the atomic coordinates and basis set and is followed by the $VEC group which contains the molecular orbitals.  They are human-readable and nicely formatted; if you're familiar with the Molpro format a Perl or Python script could make quick work of it.

Nicholas Labello
Postdoctoral Associate
Center for Drug Design
The University of Minnesota
308 Harvard Street
Minneapolis, MN 55455
(612) 626-4429



Lilianna Bryjko lb435|a|st-andrews.ac.uk wrote: 
Sent to CCL by: "Lilianna  Bryjko" [lb435.(a).st-andrews.ac.uk]
I'm looking for informations if there is any way to convert Gamess (US) orbitals to Molpro orbitals. Does maybe Gamess (US) have the option to print Molpro format orbitals.

Lilianna Bryjko
University of St AndrewsE-mail to subscribers: CHEMISTRY(a)ccl.net or use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST(a)ccl.net or use
      http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs 
Conferences: http://server.ccl.net/chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/htdig  (login: ccl, Password: search)http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/
<!-- (a)page { size: 8.5in 11in; margin-left: 1.25in; margin-right: 1.25in; margin-top: 1in; margin-bottom: 1in } P { margin-bottom: 0.08in } --> --


--------------010508030105080306050804-- From owner-chemistry@ccl.net Fri May 9 13:39:01 2008 From: "Jim Kress ccl_nospam ~~ kressworks.com" To: CCL Subject: CCL: How convert gamess orbitals to molpro orbitals Message-Id: <-36927-080509115439-8789-qFAeJuu0oV0CroGtBJXKvQ^server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 9 May 2008 10:59:19 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam{=}kressworks.com] Last time I looked, the following was the case: 1) GAMESS US does not print MOLPRO orbitals 2) even if GAMESS US did print MOLPRO orbitals, MOLPRO doesn't offer a method for reading them from the input file. Jim > -----Original Message----- > From: owner-chemistry(~)ccl.net [mailto:owner-chemistry(~)ccl.net] > Sent: Friday, May 09, 2008 6:41 AM > To: Kress, Jim > Subject: CCL: How convert gamess orbitals to molpro orbitals > > > Sent to CCL by: "Lilianna Bryjko" [lb435.(~).st-andrews.ac.uk] > I'm looking for informations if there is any way to convert > Gamess (US) orbitals to Molpro orbitals. Does maybe Gamess > (US) have the option to print Molpro format orbitals. > > Lilianna Bryjko > University of St Andrews > > > > -= This is automatically added to each message by the mailing > script =- To recover the email address of the author of the > message, please change the strange characters on the top line > to the (~) sign. You can also look up the X-Original-From: line > in the mail header.> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > From owner-chemistry@ccl.net Fri May 9 14:14:00 2008 From: "Jim Kress ccl_nospam|-|kressworks.com" To: CCL Subject: CCL: newbie question on geo opt heavy water Message-Id: <-36928-080509115446-8868-RCJJW6YIH2T2Zco3kzQUeA:_:server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 9 May 2008 11:16:50 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam]=[kressworks.com] Read this: http://link.aip.org/link/?JCPSA6/123/064104/1 And papers that it cites and that cite it. You'll find that NEO (Nuclear Electron Orbitals) will help resolve your questions. NEO's are currently implemented in GAMESS. Jim > -----Original Message----- > From: owner-chemistry_-_ccl.net [mailto:owner-chemistry_-_ccl.net] > Sent: Wednesday, May 07, 2008 5:09 PM > To: Kress, Jim > Subject: CCL: newbie question on geo opt heavy water > > > Sent to CCL by: "Joe L" [m68_x(_)hotmail.com] dear netters > > I am sorry for this newbie question, I am trying to optimize > the geometry of heavy water, the problem is with the > isotopes, regular water works fine, but somehow the bond > length and angle are the same if i use the isotopes, if > someone can give me some help, that'd be greatly appreciated. > > thanks > > joe > ---- > this is the job file > #p hf/6-31g opt > > hf/6-31g optimization of water > > 0 1 > o > h(iso=2) 1 oh > h(iso=2) 1 oh 2 aoh > > oh=0.9 > aoh=104.0 > > 298.15 1.0 > 16 > 2 > 2 > > > > -= This is automatically added to each message by the mailing > script =- To recover the email address of the author of the > message, please change the strange characters on the top line > to the _-_ sign. You can also look up the X-Original-From: line > in the mail header.> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > From owner-chemistry@ccl.net Fri May 9 15:50:01 2008 From: "Kirk Peterson kipeters%a%wsu.edu" To: CCL Subject: CCL: How convert gamess orbitals to molpro orbitals Message-Id: <-36929-080509153529-25559-DOWqUG5CRXFnaL53ml8LOQ^server.ccl.net> X-Original-From: Kirk Peterson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Fri, 9 May 2008 11:52:07 -0700 Mime-Version: 1.0 (Apple Message framework v919.2) Sent to CCL by: Kirk Peterson [kipeters%wsu.edu] For what it's worth, I'm not sure what the format should be and this can be a bit complicated depending on how each program handles symmetry and the various components of the d and higher angular momentum functions, but it is possible to read in an arbitrary matrix, i.e., orbitals, > from the input (or external) file using Molpro. One just uses the "read" directive to the matrop program. just my one cent, -Kirk On May 9, 2008, at 7:59 AM, Jim Kress ccl_nospam ~~ kressworks.com wrote: > > Sent to CCL by: "Jim Kress" [ccl_nospam{=}kressworks.com] > Last time I looked, the following was the case: > > 1) GAMESS US does not print MOLPRO orbitals > > 2) even if GAMESS US did print MOLPRO orbitals, MOLPRO doesn't offer a > method for reading them from the input file. > > Jim > > > >> -----Original Message----- >> From: owner-chemistry]|[ccl.net [mailto:owner-chemistry]|[ccl.net] >> Sent: Friday, May 09, 2008 6:41 AM >> To: Kress, Jim >> Subject: CCL: How convert gamess orbitals to molpro orbitals >> >> >> Sent to CCL by: "Lilianna Bryjko" [lb435.]|[.st-andrews.ac.uk] >> I'm looking for informations if there is any way to convert >> Gamess (US) orbitals to Molpro orbitals. Does maybe Gamess >> (US) have the option to print Molpro format orbitals. >> >> Lilianna Bryjko >> University of St Andrews >> >> >> >> -= This is automatically added to each message by the mailing >> script =- To recover the email address of the author of the >> message, please change the strange characters on the top line >> to the ]|[ sign. You can also look up the X-Original-From: line >> in the mail header.> Conferences: >> http://server.ccl.net/chemistry/announcements/conferences/ >> >> Search Messages: http://www.ccl.net/htdig (login: ccl, >> Password: search)> >> > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> >