From chemistry-request@server.ccl.net Fri Apr 4 23:19:00 2003 Received: from smtp4.server.rpi.edu ([128.113.2.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h354J0u31591 for ; Fri, 4 Apr 2003 23:19:00 -0500 Received: from rpi.edu (vpn-764.nss.rpi.edu [128.113.211.14]) by smtp4.server.rpi.edu (8.12.9/8.12.7) with ESMTP id h354IvUP005687; Fri, 4 Apr 2003 23:18:58 -0500 Message-ID: <3E8E58EF.47B0C314@rpi.edu> Date: Fri, 04 Apr 2003 23:17:51 -0500 From: "Curt M. Breneman" X-Mailer: Mozilla 4.8 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net, qsar_society@accelrys.com, chminf-l@listserv.indiana.edu Subject: Emerging Technology Symposium Competition - Deadline: April 14th. Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Scanned-By: MIMEDefang 2.28 Dear Computational Chemists and friends, This message is to remind everyone that the fourth annual Emerging Technology Symposium will take place at the New York ACS National Meeting this Fall. This COMP Division symposium is sponsored by Schrodinger, Inc who generously provides a $1,000 prize for the best presentation of the afternoon as determined by a panel of experts. Here's a copy of the announcement that's on the COMP Division website (http://membership.acs.org/C/COMP): ================= The Computers in Chemistry Division (COMP) of the ACS expects to hold the fourth annual Symposium on Emerging Technologies in ComputationalChemistry at the American Chemical Society National Meeting, New York City, USA, September 7-11, 2003. The objective of the symposium is to stimulate, reward, and publicize methodological advances in computational chemistry. The talks will be evaluated by a Panel of Experts based on the impact the research will have on the future of computational chemistry and allied sciences. The symposium will be ideal for presenting your latest and best research on new techniques and software development. Schrodinger, Inc., will again sponsor a $1000 prize for the best talk at the symposium. All are invited to participate. To participate, it is necessary to submit a regular short ACS abstract via http://oasys.acs.org/. It is also necessary to email a long (1000-word, text-only) abstract to the new organizer (Curt M. Breneman) by April 14, 2003. The talks must be original and not be repeats of talks at other ACS symposia. The long abstracts will be evaluated, and those individuals selected for an oral presentation at the symposium will be notified by the end of April. Applications for the Emerging Technologies Symposium that cannot be accepted will be rescheduled in one of the other COMP sessions at the meeting. Inquiries should sent to: Prof. Curt M. Breneman Department of Chemistry Rensselaer Polytechnic Institute Troy, NY 12180 E-mail: brenec@rpi.edu ====================================== See you in the Big Apple! Curt Breneman RPI Chemistry From chemistry-request@server.ccl.net Sat Apr 5 10:17:49 2003 Received: from web12305.mail.yahoo.com ([216.136.173.103]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h35FHnu19993 for ; Sat, 5 Apr 2003 10:17:49 -0500 Message-ID: <20030405151749.81999.qmail@web12305.mail.yahoo.com> Received: from [202.141.69.220] by web12305.mail.yahoo.com via HTTP; Sat, 05 Apr 2003 07:17:49 PST Date: Sat, 5 Apr 2003 07:17:49 -0800 (PST) From: Anirban Subject: CCL: power spectra normalization ! To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii hi ! I would like to know the following : 1> How to normalize power spectra (FFT of sampled data and its square) when a window function is used say Blackman-Harris? ( the normalization procedure given in "Numerical Recipes" are not clear to me or rather I dont know whether it is correct) 2> How do I know that my normalization is correct ? Thanx in advance Anirban __________________________________________________ Do you Yahoo!? Yahoo! Tax Center - File online, calculators, forms, and more http://tax.yahoo.com From chemistry-request@server.ccl.net Fri Apr 4 18:03:55 2003 Received: from ultra.chem.ucsb.edu ([128.111.114.119]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h34N3tu27916 for ; Fri, 4 Apr 2003 18:03:55 -0500 Received: from localhost (localhost [127.0.0.1]) by ultra.chem.ucsb.edu (Postfix) with ESMTP id EA7195035B; Fri, 4 Apr 2003 15:03:47 -0800 (PST) Received: from ultra.chem.ucsb.edu ([127.0.0.1]) by localhost (ultra [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 02370-10; Fri, 4 Apr 2003 15:03:47 -0800 (PST) Received: by ultra.chem.ucsb.edu (Postfix, from userid 3016) id D455450352; Fri, 4 Apr 2003 15:03:46 -0800 (PST) Received: from localhost (localhost [127.0.0.1]) by ultra.chem.ucsb.edu (Postfix) with ESMTP id CE8D41707D2; Fri, 4 Apr 2003 15:03:46 -0800 (PST) Date: Fri, 4 Apr 2003 15:03:46 -0800 (PST) From: John Bushnell To: VITORGE Pierre 094605 Cc: "'chemistry@ccl.net'" Subject: Re: CCL:memory limits for G98W In-Reply-To: <3808A7D2DCEAD6118B630090272872650146D7@azurite.saclay.cea.fr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN X-Virus-Scanned: by amavisd-new Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id h34N3tu27917 Are you getting errors that Gaussian doesn't have enough memory, or are you just curious why Gaussian doesn't gobble up more memory while your jobs are running? In my experience, Gaussian doesn't care how much memory you specify, as long as there is enough. I have read a warning somewhere that drastically increasing the amount of available memory can actually decrease the performance of Gaussian, though I haven't noticed that. - John On Fri, 4 Apr 2003, VITORGE Pierre 094605 wrote: > Is it possible to use more than 250Mb memory with Windows versions of > Gaussian 98 ? > I have tried %mem=300 and more, and the result was clearly only about 250Mb > was used, while I have now 1500Mb on my PC (NT4).. > > Pierre Vitorge > CEA DEN Saclay DPC/SECR/LSRM & UMR 8587 (CEA-CNRS-Universite d'Evry) > Bât.391 Pe.40a > 91191 Gif sur Yvette cedex > France > tel.(+33) 169-08-32-65, secr.: (+33)169-08-32-50, fax:(+33)169-08-32-42 > pierre.vitorge@cea.fr > http://perso.club-internet.fr/vitorgen/pierre/pierre.html > > > > -= 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 > > > > > > From chemistry-request@server.ccl.net Fri Apr 4 23:28:18 2003 Received: from smtp4.server.rpi.edu ([128.113.2.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h354SIu31689 for ; Fri, 4 Apr 2003 23:28:18 -0500 Received: from rpi.edu (vpn-764.nss.rpi.edu [128.113.211.14]) by smtp4.server.rpi.edu (8.12.9/8.12.7) with ESMTP id h354SGUP006086; Fri, 4 Apr 2003 23:28:16 -0500 Message-ID: <3E8E5B1C.95E7F6C7@rpi.edu> Date: Fri, 04 Apr 2003 23:27:09 -0500 From: "Curt M. Breneman" X-Mailer: Mozilla 4.8 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net, qsar_society@accelrys.com Subject: CCG Excellence Award Application Deadline - April 14th, 2003 for New York ACS Meeting Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Scanned-By: MIMEDefang 2.28 Dear Computational Chemistry graduate students and advisors: Applications for CCG Excellence Awards are due April 14th, 2003 for the New York ACS National Meeting! Application for these awards is a two-step process. First, an application for the Award must be submitted to the Treasurer of the COMP division for consideration. The application consists of an extended (2-page) abstract of the poster or presentation along with a letter of support from the research advisor, a two page CV, and a personal statement. Secondly, an abstract of a poster or oral presentation in the COMP program must be submitted through the ACS OASYS system for online submissions prior to the deadline for the meeting at which the awards will be presented (New York, in this case). Awardees are chosen on the basis of the quality and significance of the research to be presented, as well as the strength of the supporting letter and other materials. All graduate students are encouraged to submit applications for the Awards. Students from the same research group are encouraged to apply. Students from research groups that have won awards at previous ACS meetings are also encouraged to submit applications. Awards will be given only to those individuals making presentations, and not co-authors. For questions, contact: Prof. Curt M. Breneman; Treasurer, ACS COMP Division; RPI Department of Chemistry; 110 8th St.; Troy, NY 12180 To see photos and details of previous winners, see: http://membership.acs.org/C/COMP/CCG/ccg.html#winners From chemistry-request@server.ccl.net Sat Apr 5 11:41:25 2003 Received: from mx3.trentu.ca ([206.248.118.2]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h35GfOu20952 for ; Sat, 5 Apr 2003 11:41:25 -0500 Received: (qmail 5549 invoked by uid 504); 5 Apr 2003 16:41:00 -0000 Received: from elewars@trentu.ca by mx3.trentu.ca by uid 501 with qmail-scanner-1.14 (fsecure: 4.15/4370/2003-04-02/2003-04-02. 2003-04-02/ Clear:. Processed in 0.294262 secs); 05 Apr 2003 16:41:00 -0000 X-Qmail-Scanner-Mail-From: elewars@trentu.ca via mx3.trentu.ca X-Qmail-Scanner: 1.14 (Clear:. Processed in 0.294262 secs) Received: from unknown (HELO trentu.ca) (206.248.117.30) by mx3.trentu.ca with SMTP; 5 Apr 2003 16:41:00 -0000 Message-ID: <3E8F07EE.F0B7201E@trentu.ca> Date: Sat, 05 Apr 2003 11:44:30 -0500 From: elewars X-Mailer: Mozilla 4.79 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: "Shobe, Dave" , chemistry@ccl.net Subject: Re: CCL:TDDFT References: <5CF08BBFE6DE97478C1E76E654CAF9089C2618@lvlxch02.unitedcatalysts.com> Content-Type: multipart/alternative; boundary="------------2EB91E26EFCBA1FC82B8B869" --------------2EB91E26EFCBA1FC82B8B869 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit 2003 April 5 Hello, Re the four questions below about TDDFT: 1) Yes, G98W does TDDFT. Try for example -------------------------------- %Mem=100000000 %rwf=a,240mw,b,240mw,c,240mw,d,240mw,e,240mw,f,240mw,g,240mw,h,-1 # B3P86/6-311++G** TD=(singlets, NStates=6) Maxdisk=15360MB Oxiranylidene, calculating UV. Input: MP2/6-31G(df,p) geom. 0 1 O1 0.000000 0.778498 0.000000 C2 0.547618 -0.593873 0.000000 etc, etc -------------------------------------------- to calc the lowest 6 singlet states of a molecule. The rwf line probably isn't needed here, as scratch space should not be a problem. For the implementation of TDDFT in Gaussian see R. E. Stratman, G. E. Scuseria, and M. J. Frisch, J Chem Phys, 1998, 109, 8218. 2) Functionals and basis sets: K. B. Wiberg, R.E. Stratman, and M. J. Frisch, Chem Phys Lett, 1998, 297, 60. They used five functionals and five basis sets. The results were not strongly dependent on the functional, but B3P86 seemed best and B3LYP worst. the 6-311++G** basis was recommended. I have found AM1 geometries to give nearly as good results as the MP2/6-311+G** geometries used in this paper. 3) In calculations on methylenecyclopropene using RCIS/6-31+G*//B3LYP/6-31G*, ZINDO//AM1, and TDDFT with B3P86/6-311++G**//AM1, I found that only TDDFT matched experiment fairly well. 4) The best caveat is perhaps to first do some calculations on molecules related to those you're interested in and for which you know the experimental results. This will give you a sense of how good the calculations are. Another good idea is to read: J. Fabian et. al., THEOCHEM, 2002, 594, 41-53 (a critical evaluation of methods of calc electronic spectra). ========================= "Shobe, Dave" wrote: > > > Time-dependent density functional theory (TDDFT) has become popular > for determining electronic excitation energies (approx. = lambda max > in UV-visible spectroscopy) and excited state properties. I know very > little about this other than the name, but I would like to learn. So > here are my questions. > > 1. First, can one do TDDFT calculations using G98W? There is a TD > command listed in the manual. I suppose that your route card would be > something like this: > > # TD B3LYP 6-31G** (?) > > 2. I normally use the hybrid functional B3LYP for ground state > calculations, as it seems to be one of the better functionals for that > purpose. But would a different functinoal be recommended for TDDFT > calculations? > > 3. How good are the results compared to the CIS method? > > 4. What caveats and common beginners' mistakes are there with TDDFT? > > I will post a summary if there is interest. > > --David Shobe > Süd-Chemie Inc. > phone (502) 634-7409 > fax (502) 634-7724 > email dshobe@sud-chemieinc.com > > Don't bother flaming me: I'm behind a firewall. > --------------2EB91E26EFCBA1FC82B8B869 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit 2003 April 5

Hello,

Re the four questions below about TDDFT:

1)  Yes, G98W does TDDFT. Try for example

--------------------------------
%Mem=100000000
%rwf=a,240mw,b,240mw,c,240mw,d,240mw,e,240mw,f,240mw,g,240mw,h,-1
#  B3P86/6-311++G**  TD=(singlets, NStates=6) Maxdisk=15360MB

 Oxiranylidene, calculating UV. Input: MP2/6-31G(df,p) geom.

 0 1
    O1        0.000000    0.778498    0.000000
    C2        0.547618   -0.593873    0.000000
etc, etc
--------------------------------------------

to calc the lowest 6 singlet states of a molecule. The rwf line probably isn't needed here, as scratch space should not be a problem. For the implementation of TDDFT in Gaussian see
R. E. Stratman, G. E. Scuseria, and M. J. Frisch, J Chem Phys, 1998, 109, 8218.

2) Functionals and basis sets: K. B. Wiberg, R.E. Stratman, and M. J. Frisch, Chem Phys Lett, 1998, 297, 60. They used five functionals and five basis sets. The results were not strongly dependent on the functional, but B3P86 seemed best and B3LYP worst. the 6-311++G** basis was recommended. I have found AM1 geometries to give nearly as good results as the MP2/6-311+G** geometries used in this paper.

3) In calculations on methylenecyclopropene using RCIS/6-31+G*//B3LYP/6-31G*, ZINDO//AM1, and TDDFT with B3P86/6-311++G**//AM1, I found that only TDDFT matched experiment fairly well.

4) The best caveat is perhaps to first do some calculations on molecules related to those you're interested in and for which you know the experimental results. This will give you a sense of how good the calculations are. Another good idea is to read: J. Fabian et. al., THEOCHEM, 2002, 594, 41-53 (a critical evaluation of methods of calc electronic spectra).

=========================
"Shobe, Dave" wrote:

 

Time-dependent density functional theory (TDDFT) has become popular for determining electronic excitation energies (approx. = lambda max in UV-visible spectroscopy) and excited state properties.  I know very little about this other than the name, but I would like to learn.  So here are my questions.

1. First, can one do TDDFT calculations using G98W?  There is a TD command listed in the manual.  I suppose that your route card would be something like this:

# TD B3LYP 6-31G**  (?)

2. I normally use the hybrid functional B3LYP for ground state calculations, as it seems to be one of the better functionals for that purpose.  But would a different functinoal be recommended for TDDFT calculations?

3. How good are the results compared to the CIS method?

4. What caveats and common beginners' mistakes are there with TDDFT?

I will post a summary if there is interest.

--David Shobe
Süd-Chemie Inc.
phone (502) 634-7409
fax   (502) 634-7724
email  dshobe@sud-chemieinc.com

Don't bother flaming me: I'm behind a firewall.
 

--------------2EB91E26EFCBA1FC82B8B869-- From chemistry-request@server.ccl.net Sat Apr 5 20:55:58 2003 Received: from sccrmhc01.attbi.com ([204.127.202.61]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h361twu28837; Sat, 5 Apr 2003 20:55:58 -0500 Received: from dgallagher.cachesoftware.com (12-224-209-170.client.attbi.com[12.224.209.170]) by sccrmhc01.attbi.com (sccrmhc01) with SMTP id <20030406015557001002l9pue>; Sun, 6 Apr 2003 01:55:57 +0000 Message-Id: <5.2.0.9.0.20030405174456.027cb8c0@mail.cachesoftware.com> X-Sender: X-Mailer: QUALCOMM Windows Eudora Version 5.2.0.9 Date: Sat, 05 Apr 2003 17:55:12 -0800 To: chemistry@ccl.net From: David Gallagher Subject: New Windows-based tools for life-sciences Cc: chemistry-request@ccl.net Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_1539566==.ALT" --=====================_1539566==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed New BioCAChe & BioMedCAChe 6.0 release on Windows The CAChe Group of Fujitsu is pleased to announce a new release of BioMedCAChe version 6.0 and the new BioCAChe 6.0 (= BioMedCAChe without QSAR). BioMedCAChe 6.0 Enhancements: * Identify conserved residues with Automatic Sequence Alignment * Locate potential binding sites on proteins with Crevice Maps * Identify active sites with automatic sequence matching * Display hydrophilic & hydrophobic areas on protein Surfaces * Simplify ligand design & modification with Ligand Pocket Surfaces * Compare ligand docking scores with Automatic H-bond & Bump Labeling * Simplify analysis of proteins with Ribbons & Curls Displays * More accurate protein/ligand geometries with new MM & MD parameters Also new for 6.0 is a Protein Tutorial with chapters on: * Importing and Cleaning Protein Crystal Structures * Viewing and Analyzing Proteins, Ligands, and their Complexes * Docking Ligands into Proteins * Discovering Active Sites of Homologous Proteins by Sequence Alignment Customers with current support contracts for BioMedCAChe can expect to receive a free copy of the new version by mail during the next few weeks. CAChe users without support may upgrade for a nominal fee. To find out more, contact sales@cachesoftware.com or visit www.CACheSoftware.com --=====================_1539566==.ALT Content-Type: text/html; charset="us-ascii" New BioCAChe & BioMedCAChe 6.0 release on Windows

The CAChe Group of Fujitsu is pleased to announce a new release of BioMedCAChe version 6.0 and the new BioCAChe 6.0 (= BioMedCAChe without QSAR).

BioMedCAChe 6.0 Enhancements:
*  Identify conserved residues with Automatic Sequence Alignment
*  Locate potential binding sites on proteins with Crevice Maps
*  Identify active sites with automatic sequence matching
*  Display hydrophilic & hydrophobic areas on protein Surfaces
*  Simplify ligand design & modification with Ligand Pocket Surfaces
*  Compare ligand docking scores with Automatic H-bond & Bump Labeling
*  Simplify analysis of proteins with Ribbons & Curls Displays 
*  More accurate protein/ligand geometries with new MM & MD parameters

Also new for 6.0 is a Protein Tutorial with chapters on:
*  Importing and Cleaning Protein Crystal Structures
*  Viewing and Analyzing Proteins, Ligands, and their Complexes
*  Docking Ligands into Proteins
*  Discovering Active Sites of Homologous Proteins by Sequence Alignment

Customers with current support contracts for BioMedCAChe can expect to receive a free copy of the new version by mail during the next few weeks.  CAChe users without support may upgrade for a nominal fee.  To find out more, contact sales@cachesoftware.com or visit www.CACheSoftware.com


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