From chemistry-request@server.ccl.net Sat Aug 17 19:33:18 2002 Received: from mailbox.engr.sc.edu ([129.252.21.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7HNXIo02944 for ; Sat, 17 Aug 2002 19:33:18 -0400 Received: from kashanluwiswan (kashanluwiswan.ee.sc.edu [129.252.22.146]) by mailbox.engr.sc.edu with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2656.59) id QWZRPVDK; Sat, 17 Aug 2002 19:17:44 -0400 Message-ID: <012a01c24643$454ca800$9216fc81@engr.sc.edu> From: "Luis Cordova" To: References: Subject: Re: CCL:Solaris cluster Date: Sat, 17 Aug 2002 18:10:23 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Let me add that in sun cluster facilities the norm is dmake -j 16 and that is in 16 CPUs. ----- Original Message ----- From: "Kenneth Geisshirt" To: "Computational Chemistry List" Sent: Wednesday, August 14, 2002 6:36 AM Subject: CCL:Solaris cluster On Wed, 14 Aug 2002, Szilveszter Juhos wrote: > What I need is not a queueing system like GridEngine > or Condor but something that can manage "gmake -j 16" on 4 machines with 4 > cpus each. You should take a look at ANTS: http://unthought.net/antsd Kneth -- Kenneth Geisshirt, M.Sc., Ph.D. http://kenneth.geisshirt.dk Grøndals Parkvej 2A, 3. sal kenneth@geisshirt.dk DK-2720 Vanløse +45 38 87 78 38 -= 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 Sat Aug 17 10:19:46 2002 Received: from web12804.mail.yahoo.com ([216.136.174.39]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g7HEJko19380 for ; Sat, 17 Aug 2002 10:19:46 -0400 Message-ID: <20020817141946.63152.qmail@web12804.mail.yahoo.com> Received: from [61.9.73.249] by web12804.mail.yahoo.com via HTTP; Sat, 17 Aug 2002 07:19:46 PDT Date: Sat, 17 Aug 2002 07:19:46 -0700 (PDT) From: amor san juan Subject: AutoDock Tools (ADT) To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi all AutoDock community, Have anyone viewed *.dlg & macromolecule(>4000atoms) through ADT. I can only view small proteins of about 1000 atoms with the ligand. I appreciate any comments. Amor __________________________________________________ Do You Yahoo!? HotJobs - Search Thousands of New Jobs http://www.hotjobs.com From chemistry-request@server.ccl.net Sun Aug 18 10:05:17 2002 Received: from web14502.mail.yahoo.com ([216.136.224.65]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g7IE5Ho28963 for ; Sun, 18 Aug 2002 10:05:17 -0400 Message-ID: <20020818140516.2085.qmail@web14502.mail.yahoo.com> Received: from [129.22.7.147] by web14502.mail.yahoo.com via HTTP; Sun, 18 Aug 2002 07:05:16 PDT Date: Sun, 18 Aug 2002 07:05:16 -0700 (PDT) From: Suman Chakravarti Subject: Algorithms for 2D to 3D conversion of rings To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCLers Does anybody has any idea of any free source code in C or FORTRAN for converting connectivity table of structures containing rings (fused, bridged etc) to 3D coordinates using simple rules and without molecular mechanics. sincerely Suman *************************************************** Suman K. Chakravarti Chemistry Department Case Western Reserve University Cleveland, OH 44106, USA *************************************************** __________________________________________________ Do You Yahoo!? HotJobs - Search Thousands of New Jobs http://www.hotjobs.com From chemistry-request@server.ccl.net Fri Aug 16 13:50:12 2002 Received: from seraph2.grc.nasa.gov ([128.156.10.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7GHoBo27589 for ; Fri, 16 Aug 2002 13:50:11 -0400 Received: from lombok-fi.lerc.nasa.gov (lombok-fi.lerc.nasa.gov [139.88.112.33]) by seraph2.grc.nasa.gov (Postfix) with ESMTP id D14CFC699D for ; Fri, 16 Aug 2002 13:50:06 -0400 (EDT) Received: from apataki-fi.lerc.nasa.gov (apataki-fi.lerc.nasa.gov [139.88.112.35]) by lombok-fi.lerc.nasa.gov (NASA GRC 8.12.3/8.12.3) with ESMTP id g7GHo6Bg022570; Fri, 16 Aug 2002 13:50:06 -0400 (EDT) Received: from mzehe.grc.nasa.gov (mzehe.lerc.nasa.gov [139.88.15.36]) by apataki-fi.lerc.nasa.gov with ESMTP (8.8.8+Sun/2.20-grc) id NAA07986; Fri, 16 Aug 2002 13:50:05 -0400 (EDT) Message-Id: <5.1.0.14.2.20020816133036.00a793b0@popserve.grc.nasa.gov> X-Sender: mszehe@popserve.grc.nasa.gov (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Fri, 16 Aug 2002 13:49:59 -0400 To: knauerc From: Michael J Zehe Subject: Re: CCL:SUMMARY:Equilibrium Constants Cc: chemistry@ccl.net In-Reply-To: <3D52C65A.1728A54E@georgetown.edu> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_23719691==_.ALT" --=====================_23719691==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Dear Everyone: Many people have communicated to say that they can't hook up to the NASA Glenn CEA site referenced below because the link was not working: the link should have been without the final character, use : http://www.grc.nasa.gov/www/ceaweb Others have commented about the convenience of the PFC program for obtaining thermodynamic functions and have asked for details about its input data. The CEA database consists of blocks of coefficients to the following 'Shomate plus" equation: Cpo (T)/R = a1T-2 + a2T-1 + a3 + a4T + a5T2 + a6T3+ a7T4 plus integration constants for H and S. This form was chosen because it allows accurate fits over a wide temperature range. Input data is taken > from standard compilations, from the literature, or calculated from published spectroscopic data. The data are updated almost continuously and documented thoroughly. CEA and its database are heavily used by the aerodynamics communiity for rocket and jet engine design and analysis, and the database has grown from 42 species in its first published version (in 1951) to the current 2000. Much of this information is contained at http://www.grc.nasa.gov/www/ceaweb Also soon available will be a report NASA/TP-2002-211556, available from Ms.McBride at the above site. At 03:28 PM 08/08/2002 -0400, knauerc wrote: >Thanks to everyone for your help, and my apologies for being >so late in posting this summary of responses. > >My question was: > >Does anyone know where I can find good data for the equilibrium >constants, (as a function of temperature), for the reactions: > >H2 + Cl2 = 2HCl > >and > >H2 + Br2 = 2HBr > >The answers I received were: > >1) Abhishek Jha (ajha@midway.uchicago.edu) > >Hi! >Try www.nist.gov >I have used this before so I am sure you will get what you are looking >for. Best of luck! > >Cheers! >Abhishek Jha > > >2) Wayne Steinmetz (WES04747@pomona.edu) > >Consider using the JANF Thermochemical Tables. > >3) Bill Smith (bilsmith@uoguelph.ca) > >Apart from standard tables like the JANAF Tables >(CHASE,M.,Jr.,1998, {\it NIST-JANAF Thermochemical Tables, 4th ed., J. >Phys. and >Chem. Reference Data Monograph No. 9,} (Am. Chem. Society, Am. Inst. >Physics).Data, you can get a lot of this data from the free Lite version >of the >reaction equilibrium software package EQS4WIN, available at > >http://www.mathtrek.com > >4) Chuck McFarland (cwm001@apk.net) > >Given that enthalpy and entropy easily lead to free energies, which in >turn lead >to equilibrium constants, and that Shomate equation coefficients give >temperature dependence, most, if not all, of what you need is at > >http://webbook.nist.gov/chemistry/ > >5) David Shobe (dshobe@sud-chemieinc.com) > >The NIST WebBook (http://webbook.nist.gov/chemistry/) has thermochemical >data as >a function of temperature, and you can calculate equilibrium constants in the >usual way. > >(Also note that the answers and necessary data sets will differ >considerably for >gas-phase and aqueous-phase equilibrium constants). > >6) Viswanathan Balakrishnan (bviswan@chem1.chem.dal.ca) > >The equilibrium constants can be calculated from the thermodynamic data >available at http://webbook.nist.gov/chemistry/ > >7) Michael J. Zehe (Michael.J.Zehe@grc.nasa.gov) > >A convenient source of up-to-date thermodynamic data in an easily-used form is >the program PFC, at http://cea.grc.nasa.gov/. PFC allows the user to get >accurate data for over 2000 species contained in the NASA Glenn, (formerly >NASA >Lewis),database documented in NASA TP-2002-211556 and at >http://www>.grc.nasa.gov/www/ceaweb>. This database has been maintained and >documented for almost 50 years by Ms. Bonnie Mcbride et al at NASA Glenn in >support of the NASA chemical equilibrium program CEA. > > >-= 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 Michael J. Zehe (216) 433-5833 --=====================_23719691==_.ALT Content-Type: text/html; charset="us-ascii" Dear Everyone:
Many people have communicated to say that they can't hook up to the NASA Glenn CEA site referenced below because the link was not working:  the link should have been without the final character, use : http://www.grc.nasa.gov/www/ceaweb

Others have commented about the convenience of the PFC program for obtaining thermodynamic functions and have asked for details about its input data.  The CEA database consists of blocks of coefficients to the following 'Shomate plus" equation:

Cpo (T)/R  = a1T-2 + a2T-1 + a3 + a4T + a5T2 + a6T3+ a7T4  

plus integration constants for H and S. This form was chosen because it allows accurate fits over a wide temperature range.  Input data is taken from standard compilations, from the literature, or calculated from published spectroscopic data.  The data are updated almost continuously and documented thoroughly. 

CEA and its database are heavily used by the aerodynamics communiity for rocket and jet engine design and analysis, and the database has grown from 42 species in its first published version (in 1951) to the current 2000.  Much of this information is contained at

Also soon available will be  a report  NASA/TP-2002-211556, available from Ms.McBride at the above site.



At 03:28 PM 08/08/2002 -0400, knauerc wrote:
Thanks to everyone for your help, and my apologies for being
so late in posting this summary of responses.

My question was:

Does anyone know where I can find good data for the equilibrium
constants, (as a function of temperature), for the reactions:

H2 + Cl2 = 2HCl

and

H2 + Br2 = 2HBr

The answers I received were:

1) Abhishek Jha (ajha@midway.uchicago.edu)

Hi!
Try www.nist.gov
I have used this before so I am sure you will get what you are looking
for.  Best of luck!

Cheers!
Abhishek Jha


2) Wayne Steinmetz (WES04747@pomona.edu)

Consider using the JANF Thermochemical Tables.

3) Bill Smith (bilsmith@uoguelph.ca)

Apart from standard tables like the JANAF Tables
(CHASE,M.,Jr.,1998, {\it NIST-JANAF Thermochemical Tables, 4th ed., J. Phys. and
Chem. Reference Data Monograph No. 9,} (Am. Chem. Society, Am. Inst.
Physics).Data, you can get a lot of this data from the free Lite version of the
reaction equilibrium software package EQS4WIN, available at

http://www.mathtrek.com

4) Chuck McFarland (cwm001@apk.net)

Given that enthalpy and entropy easily lead to free energies, which in turn lead
to equilibrium constants, and that Shomate equation coefficients give
temperature dependence, most, if not all, of what you need is at

http://webbook.nist.gov/chemistry/

5) David Shobe (dshobe@sud-chemieinc.com)

The NIST WebBook (http://webbook.nist.gov/chemistry/) has thermochemical data as
a function of temperature, and you can calculate equilibrium constants in the
usual way.

(Also note that the answers and necessary data sets will differ considerably for
gas-phase and aqueous-phase equilibrium constants).

6) Viswanathan Balakrishnan (bviswan@chem1.chem.dal.ca)

The equilibrium constants can be calculated from the thermodynamic data
available at http://webbook.nist.gov/chemistry/

7) Michael J. Zehe (Michael.J.Zehe@grc.nasa.gov)

A convenient source of up-to-date thermodynamic data in an easily-used form is
the program PFC, at http://cea.grc.nasa.gov/. PFC allows the user to get
accurate data for over 2000 species contained in the NASA Glenn, (formerly NASA
Lewis),database documented in NASA TP-2002-211556 and at
http://www>.grc.nasa.gov/www/ceaweb>. This database has been maintained and
documented for almost 50 years by Ms. Bonnie Mcbride et al at NASA Glenn in
support of the NASA chemical equilibrium program CEA.


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Michael J. Zehe
(216) 433-5833 --=====================_23719691==_.ALT-- From chemistry-request@server.ccl.net Sun Aug 18 20:46:20 2002 Received: from hotmail.com ([64.4.21.93]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7J0kKI02999 for ; Sun, 18 Aug 2002 20:46:20 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Sun, 18 Aug 2002 17:46:14 -0700 Received: from 203.116.61.131 by lw14fd.law14.hotmail.msn.com with HTTP; Mon, 19 Aug 2002 00:46:14 GMT X-Originating-IP: [203.116.61.131] From: "xu xiao feng" To: chemistry@ccl.net Subject: Tinker Date: Mon, 19 Aug 2002 00:46:14 +0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 19 Aug 2002 00:46:14.0635 (UTC) FILETIME=[D236B3B0:01C24719] Dear CCL members, I need your help. When I use Tinker to optimize a carbon nanotube model, I got a negative result. Anybody can help to explain what's the meaning of that? Force Field : MM2 Atom Type : C 22 Best regards, Xu Xiao Feng _________________________________________________________________ Chat with friends online, try MSN Messenger: http://messenger.msn.com