From chemistry-request@server.ccl.net Thu Sep 16 17:13:52 1999 Received: from sparrow.prod.itd.earthlink.net (sparrow-e.prod.itd.earthlink.net [207.217.118.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA05729 for ; Thu, 16 Sep 1999 17:13:50 -0400 Received: from lrz.de (1Cust251.tnt1.rancho-cucamonga.ca.da.uu.net [208.251.225.251]) by sparrow.prod.itd.earthlink.net (8.9.3/8.9.3) with ESMTP id OAA04685; Thu, 16 Sep 1999 14:07:25 -0700 (PDT) Received: (from eugene.leitl@localhost) by lrz.de (8.8.8/8.8.8) id OAA17315; Thu, 16 Sep 1999 14:04:48 -0700 Resent-From: Eugene Leitl Resent-Message-ID: <14305.23407.967310.117084@lrz.de> Resent-Date: Thu, 16 Sep 1999 14:04:47 -0700 (PDT) Resent-To: , , , , Message-Id: <001a01xxxbf006d$42126400$5f21328f@sgi-onyx-1> 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 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Precedence: bulk From: To: Subject: YASARA Date: Thu, 16 Sep 1999 19:55:56 +0200 From: "Elmar" Dear PDB Users, during the past 18 months, I have spent a lot of time and patience on the development of an interactive real-time molecular-modeling and -dynamics program called YASARA ("Yet Another Scientific Artificial Reality Application"). The project was my master's thesis at the Institute of Microbiology / University of Graz, Austria and currently contains 60000 lines C- and Assembler-code. With YASARA as some sort of "qualification proof", I am now searching for a PhD position in the area of bioinformatics. All the details can be found at my homepage: http://www-stud.kfunigraz.ac.at/~kriegere Comments that are too specific for the public can be directed to: elmar.krieger@kfunigraz.ac.at Some additional facts about YASARA, just in case you want to read more before activating your browser: * The main goal was the optimization of the price/performance ratio: YASARA has been developed for Intel/AMD processors, either single PCs or linked clusters of many computers. * The FTS3D ("Faster Than a Snail" 3D)-engine is aimed at the fluid display of large molecules (>30000 atoms, space fill or wire frame) in true 3D (shutter glasses). * Molecules can be moved around in three dimensions using an ultrasonic pointer. * The YASARA force field is based on molecule-trees, statistical analysis of protein structures and off-center point charges. * A virtual ribosome helps to calculate protein folds. * NMR: Protein structures can be calculated based on NOESY distance restraints and the YASARA force field. * Fold prediction: A crude method for bridging the gap between secondary and tertiary structure has been established. * Automated docking with three degrees of freedom: YASARA searches for the binding site of alpha helices inside the major DNA groove. * Parallel molecular dynamics with an interactive real-time display, using freely importable force fields (e.g. AMBER). It is possible to pull atoms/molecules around, allowing the interactive modeling of large complexes. Thanks a lot for your attention and transmission bandwidth, best greetings from Austria, Elmar Krieger *** Details on how to be removed from this list as well as an *** *** archive of recent postings are available at *** *** http://www.rcsb.org/pdb/forum.html *** From chemistry-request@server.ccl.net Thu Sep 16 18:03:30 1999 Received: from cornelius.INS.CWRU.Edu (root@cornelius.INS.CWRU.Edu [129.22.8.216]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA06172 for ; Thu, 16 Sep 1999 18:03:30 -0400 Received: from raman2.cwru.edu (chem51374.CHEM.CWRU.Edu [129.22.200.174]) by cornelius.INS.CWRU.Edu with SMTP (8.8.8+cwru/CWRU-3.6) id RAA05094; Thu, 16 Sep 1999 17:57:12 -0400 (EDT) (from hxt10@po.cwru.edu for ) Message-ID: <002901bf0097$276d4f00$aec81681@cwru.edu> From: "Gavin Tsai" To: Subject: isotope shift Date: Thu, 16 Sep 1999 17:59:38 -0500 Hi, CCLers: This is a general question for isotope shift vibration band assignment = of ab initio calculations.... I calculated the isotope shift of stilbene vibration at DFT level and = have to assign the shift after isotope substituted. The symmetry, = intensity, and vibration motions are used to do the assignment. Some of the modes are very easy to assigned, but some are mixed together = and very difficult to do the assignment. Is there anyone have experience = in doing this kind of assignment? Any comment and suggestion is welcomed and appreciated. Thanks Gavin=20 N:Tsai;Hui-Hsu (Gavin) FN:Hui-Hsu (Gavin) Tsai NICKNAME:Gavin ORG:CWRU, Chemistry Department TITLE:Ph.D. Candidate NOTE;ENCODING=3DQUOTED-PRINTABLE:Do molecules calculate the chemical = reaction laws before they decide=3D0D=3D0Aho=3D w to react to each others?=3D0D=3D0A TEL;HOME;VOICE:216-229-5913 ADR;HOME:;;2416 Derbyshire Road;Cleveland;OH;44106;USA LABEL;HOME;ENCODING=3DQUOTED-PRINTABLE:2416 Derbyshire = Road=3D0D=3D0ACleveland, OH 44106=3D0D=3D0AUSA X-WAB-GENDER:2 EMAIL;PREF;INTERNET:hxt10@po.cwru.edu From chemistry-request@server.ccl.net Fri Sep 17 06:06:20 1999 Received: from mailrelay2.lrz-muenchen.de (mailrelay2.lrz-muenchen.de [129.187.254.102]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA08705 for ; Fri, 17 Sep 1999 06:06:10 -0400 Received: from ruppert.phys.chemie.tu-muenchen.de by mailrelay2.lrz-muenchen.de for @dfvgate.lrz-muenchen.de:chemistry@ccl.net; Fri, 17 Sep 1999 11:59:29 +0200 Received: from physik.tu-muenchen.de by ruppert.phys.chemie.tu-muenchen.de via ESMTP (940816.SGI.8.6.9/930416.SGI) for id LAA17834; Fri, 17 Sep 1999 11:59:28 +0200 Sender: tmehnert@physik.tu-muenchen.de Message-Id: <37E210FD.DA97AFB2@physik.tu-muenchen.de> Date: Fri, 17 Sep 1999 11:59:27 +0200 From: Mehnert Thomas X-Mailer: Mozilla 4.04 [en] (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Summary: Jaguar against Gaussian Content-Type: multipart/alternative; boundary="------------D286A8CC4BBD6498EC43CFE2" --------------D286A8CC4BBD6498EC43CFE2 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi alltogether, Some times ago I posted a question: "Does anybody have gained experience with the Jaguar and/or Titan program? Do they calculate molecular geometries and frequencies substantially faster than GAUSSIAN 94/98?" Here is the summary of the answers. Thanks to all who replied. -------------------------------------------------------------- I've been using Jaguar for DFT calculations on transition metal complexes for about a year now and have been very happy with it. In my hands I've found much faster than G94 for both geometry optimization and frequency calculations. I have to note that for the systems I've been working with the frequency calculations are done numerically instead of analytically but for my purposes they're fine. Schrodinger's tech support are also quite helpfull and fast. -------------------------------------------------------------- I've used jaguar a fair bit, as well as gaussian 98, and have found jaguar to be significantly faster for the same systems at the same level of theory. This is on PC's runnning linux, i don't have experience with windows, which from you're query about titan, i suppose you are using. -------------------------------------------------------------- Several years ago I ran a few B3LYP comparisons (single point, no optimizations) between Jaguar and G94 on small molecules. Jaguar was much faster. My guess is that this speed difference would be maintained on larger molecules, but I did not do the test. -------------------------------------------------------------- I've found Jaguar to be 7 - 10 times faster than G98 for geometry optimisations and frequency calculations of organometallic compounds. Jobs were run on Linux/Intel or Dec Alphas. -------------------------------------------------------------- Bye Th. Mehnert --------------D286A8CC4BBD6498EC43CFE2 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi alltogether,

Some times ago I posted a question:

"Does anybody have gained experience with the Jaguar and/or Titan
program?
Do they calculate molecular geometries and frequencies substantially
faster than GAUSSIAN 94/98?"
 

Here is the summary of the answers. Thanks to all who replied.

--------------------------------------------------------------
I've been using Jaguar for DFT calculations on transition metal complexes for about a year now and have
been very happy with it. In my hands I've found much faster than G94 for both geometry optimization and
frequency calculations. I have to note that for the systems I've been working with the frequency calculations
are done numerically instead of analytically but for my purposes they're fine. Schrodinger's tech support
are also quite helpfull and fast.
--------------------------------------------------------------
I've used jaguar a fair bit, as well as gaussian 98, and have found
jaguar to be significantly faster for the same systems at the same level
of theory.  This is on PC's runnning linux, i don't have experience with
windows, which from you're query about titan, i suppose you are using.
--------------------------------------------------------------
Several years ago I ran a few B3LYP comparisons (single point, no optimizations) between Jaguar and G94
on small molecules. Jaguar was much faster. My guess is that this speed difference would be maintained on
larger molecules, but I did not do the test.
--------------------------------------------------------------
I've found Jaguar to be 7 - 10 times faster than G98 for geometry
optimisations and frequency calculations of organometallic compounds.  Jobs
were run on Linux/Intel or Dec Alphas.
--------------------------------------------------------------
 

Bye

Th. Mehnert
 
  --------------D286A8CC4BBD6498EC43CFE2-- From chemistry-request@server.ccl.net Fri Sep 17 11:43:14 1999 Received: from cerberus.ulaval.ca (cerberus.ulaval.ca [132.203.250.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA11042 for ; Fri, 17 Sep 1999 11:43:14 -0400 Received: from fluor.chm.ulaval.ca (fluor.chm.ulaval.ca [132.203.70.9]) by cerberus.ulaval.ca (8.9.3/8.9.3) with ESMTP id LAA18884 for ; Fri, 17 Sep 1999 11:48:07 -0400 (EDT) Received: (from anh@localhost) by fluor.chm.ulaval.ca (8.6.12/8.6.12) id JAA08812 for chemistry@ccl.net; Fri, 17 Sep 1999 09:33:06 -0400 From: "Nguyen N. Anh" Message-Id: <9909170933.ZM8810@fluor.chm.ulaval.ca> Date: Fri, 17 Sep 1999 09:33:02 -0400 X-Mailer: Z-Mail (3.2.1 6apr95 MediaMail) To: chemistry@ccl.net Subject: complex-valued scf Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear cclers, I'm interested in doing complex-valued scf calculations. Can anyone point me to recent references (if any) or packages? Thank you very much. -- Nguyen Nam Anh Quebec, Canada E-mail: anh@chm.ulaval.ca WWW: http://promethium.chm.ulaval.ca/~anh/ From chemistry-request@server.ccl.net Fri Sep 17 14:03:00 1999 Received: from terra.ifi.unicamp.br (terra.ifi.unicamp.br [143.106.6.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA11588 for ; Fri, 17 Sep 1999 14:02:54 -0400 Received: from ifi.unicamp.br (lua [143.106.6.13]) by terra.ifi.unicamp.br (8.9.3/8.9.3) with ESMTP id OAA10882 for ; Fri, 17 Sep 1999 14:54:17 -0300 (BSC) Received: (from daemon@localhost) by ifi.unicamp.br (8.9.3/8.9.3) id OAA12220 for ; Fri, 17 Sep 1999 14:54:05 -0300 (EST) Received: from gauss.ifi.unicamp.br(143.106.72.139), claiming to be "ifi.unicamp.br" via SMTP by lua.ifi.unicamp.br, id smtpdAAAa002ys; Fri Sep 17 14:54:02 1999 Message-ID: <37E2819B.419CCF89@ifi.unicamp.br> Date: Fri, 17 Sep 1999 14:59:55 -0300 From: =?iso-8859-1?Q?M=E1rcio?= Cyrillo Organization: unicamp X-Mailer: Mozilla 4.61 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: Computational Chemistry List Subject: mopac Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear All, Does anybody of you know if there is a parallelized version of the *FREE* MOPAC program, like version 6 or 7 and where I can get it? Thanks in advance, Marcio.