From chemistry-request@ccl.net Wed Sep 24 08:37:57 2003 -0400 Date: Wed, 24 Sep 2003 14:37:33 +0200 Message-ID: <3F6F5F6200003C84^at^ims1b.cp.tin.it> From: sa.cosco^at^virgilio.it Subject: CCL:plot RMSD vs time with INSIGHT II To: chemistry^at^ccl.net Hi all, does anybody know how to construct a RMSD vs time plot for a protein dyna= mics with INSIGHT II? I already know how to construct a graph with simple parameters such as fr= ame vs distance and so on.. but I run in difficoulties in selecting the RMSD as y parameter for my plot. thanks in advance for your help sandro From chemistry-request@ccl.net Tue Sep 23 18:54:44 2003 Received: from mail.uh.edu (SanJacinto.Mail.uh.edu [129.7.235.116]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8NMsDmK024078 for ; Tue, 23 Sep 2003 18:54:13 -0400 Received: from conversion-daemon by mail.uh.edu (Sun Internet Mail Server sims.4.0.2001.07.26.11.50.p9) id <0HLO00601VM3DA=at=mail.uh.edu> for chemistry=at=ccl.net; Tue, 23 Sep 2003 17:54:03 -0500 (CDT) Received: from localhost (Colorado.Mail.UH.EDU [129.7.235.114]) by mail.uh.edu (Sun Internet Mail Server sims.4.0.2001.07.26.11.50.p9) with ESMTP id <0HLO0066LVM25J=at=mail.uh.edu> for chemistry=at=ccl.net; Tue, 23 Sep 2003 17:54:02 -0500 (CDT) Date: Tue, 23 Sep 2003 17:54:02 -0500 (CDT) From: Niharendu.Choudhury=at=mail.uh.edu Subject: How to calculate delta G from a MD simulation To: chemistry=at=ccl.net Message-id: <482494436.1064357642080.JavaMail.root@localhost> MIME-version: 1.0 X-Mailer: Sun(TM) Web Access 1.2 Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 7BIT X-Spam-Status: No, hits=0.8 required=7.0 tests=NO_REAL_NAME version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi all I have two solute molecules fixed in a water box and I am performing MD simulation. I would like to calculate the the free energy difference as a function of r, the distance between two fixed solutes. How can I do that with the Free Energy Perturbation (FEP) technique(simplest way) > from my MD simulation? Niharendu Choudhury From chemistry-request@ccl.net Wed Sep 24 03:12:53 2003 Received: from hawk.dcu.ie (mail.dcu.ie [136.206.1.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8O7CLmK025004 for ; Wed, 24 Sep 2003 03:12:22 -0400 Received: from [136.206.1.18] by hawk.dcu.ie with HTTP; Wed, 24 Sep 2003 08:12:20 +0100 Date: Wed, 24 Sep 2003 08:12:20 +0100 Message-ID: <3F6B7AEB00002A2C=at=hawk.dcu.ie> From: "Noel O'Boyle" Subject: GaussSum 0.4 available To: chemistry=at=ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h8O7CrmK025121 Hello all, GaussSum 0.4 is now available from http://gausssum.sourceforge.net. This is a FREE parser for Gaussian output files which can be used to do the following: -display all lines containing a certain phrase -follow the progress of the SCF convergence -follow the progress of a geometry optimisation -extract molecular orbital information, including contributions of groups of atoms to the molecular orbitals -plot the density of states spectrum (and the partial density of states, in the case of groups of atoms) -extract information on the UV-Vis transitions, including the change in the charge density of groups of atoms -plot the UV-Vis spectrum -automate the creation of electron density difference maps, which visually show the change in charge density associated with a given electronic transition -extract information on IR and Raman vibrations -plot the IR and Raman spectra, which may be scaled Feedback and bug reports are appreciated. Noel O'Boyle Noel O'Boyle Han Vos Research Group School of Chemical Sciences Dublin City University http://www.dcu.ie/~chemist/Staffpages/han_vos.htm From chemistry-request@ccl.net Tue Sep 23 12:51:34 2003 Received: from smtp.csc.fi (smtp.csc.fi [193.166.0.106]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8NGp2mK008861 for ; Tue, 23 Sep 2003 12:51:03 -0400 Received: from tylypahka (rhols63.adsl.netsonic.fi [194.29.198.63]) by smtp.csc.fi (CSC-Sendmail) with ESMTP id h8NGowUC005906 for ; Tue, 23 Sep 2003 19:50:58 +0300 From: "Leif Laaksonen" To: Subject: gOpenMol version 2.30 is now available! Date: Tue, 23 Sep 2003 19:51:04 +0300 Message-ID: <000401c381f2$e0d26760$ba1c7b0a@tylypahka> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.4510 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 Importance: Normal X-DCC-FUNET-Metrics: pobox5.csc.fi 32702; Body=1 Fuz1=1 Fuz2=1 X-Scanned-By: MIMEDefang 2.37 X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h8NGpYmK008912 Hi! Version 2.30 of the computational chemistry display and analysis toolbox program gOpenMol is now available. Updated web pages available at http://www.csc.fi/gopenmol/. The release version 2.30 is available at: http://www.csc.fi/gopenmol/distribute/ The current release has some new features and a significant part of the code has been rewritten. The Linux version should now be easy to remake and it should be quite easy to port gOpenMol to any Unix platform. If you you have graphics hardware support on Linux for OpenGL gOpenMol should now support your library. The graphics display speed has also been improved in general. My sincere thanks to Scott L. Anderson, Kevin J. Boyd and Eero Hdkkinen for their coding and support. Remember, be happy! Regards, -leif laaksonen ------------------------------------------------------------------------ Leif Laaksonen, Development Manager, CSC, P.O. Box 405, FIN-02101 Espoo, Finland, (Street address: Tekniikantie 15 a D), phone: +358-9-4572378, fax: +358-9-4572302, CSC is the Finnish IT Center for Science, www.csc.fi. E-mail: Leif.Laaksonen=at=csc.fi ------------------------------------------------------------------------ From chemistry-request@ccl.net Wed Sep 24 00:49:42 2003 Received: from front3.chartermi.net (front3.chartermi.net [24.213.60.109]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8O4nAmK012595 for ; Wed, 24 Sep 2003 00:49:10 -0400 Received: from [24.236.135.230] (HELO master.bw01.kressworks.com) by front3.chartermi.net (CommuniGate Pro SMTP 3.5.9a) with ESMTP id 326728846 for chemistry=at=ccl.net; Wed, 24 Sep 2003 00:48:59 -0400 Content-Type: text/plain; charset="iso-8859-1" From: Jim Kress To: chemistry=at=ccl.net Subject: Re: CCL:B3LYP functional specification of constants Date: Wed, 24 Sep 2003 00:41:50 +0000 User-Agent: KMail/1.4.3 References: <200309200238.18038.ccl=at=kressworks.com> In-Reply-To: <200309200238.18038.ccl=at=kressworks.com> MIME-Version: 1.0 Message-Id: <200309240041.50249.jimkress=at=kressworks.com> X-Spam-Status: No, hits=-1.7 required=7.0 tests=DATE_IN_PAST_03_06,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_KMAIL version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h8O4ngmK012674 My original question: > While investigating prior to doing some extensive B3LYP calculations, I've > noticed that GAMESS and MOLPRO use 0.08 times the Slater Exchange in the > B3LYP functional while NWCHEM and GAUSSIAN use 0.8. Which is correct? Received one reply. Thanks to Huub van Dam for his response (given at the end of this note). In addition, from the GAMESS manual: > Note that B3LYP in GAMESS is based in part on the VWN5 > correlation functional. Since there are five formulae > in the VWN paper for local correlation, other programs > may use other formulae, and therefore generate different > B3LYP energies. For example, NWChem's manual says it uses > the "VWN 1 functional with RPA parameters as opposed to the > prescribed Monte Carlo parameters", but NWChem can be made > to use the VWN5 formula by > xc HFexch 0.20 slater 0.80 becke88 nonlocal 0.72 > lyp 0.81 vwn_5 0.19 > If you use some other program, its B3LYP energy will be > different from GAMESS if it does not employ VWN5. So we see there is no unique definition for the b3lyp functional. This seems a recipie for confusion but hey, what do I know? Note: MOLPRO and GAMESS (as of their current incarnations) use the same definition for the b3lyp functional. Jim > I think MOLPRO uses 0.8 times the Slater Exchange functional as well. The > confusion stems from what people call the Becke '88 functional. In MOLPRO > the Becke '88 functional is defined as > > B88 = rho^(4/3)*(c+dB88) > > where dB88 is the gradient enhancement factor and c*rho^(4/3) is the Slater > functional. In other codes the functional is defined as > > B88' = rho^(4/3)*dB88 > > without the Slater functional term. Of course the parameters you have to > use to arrive at the correct B3LYP expression depend on which definition of > the Becke '88 you use. > > A different matter is that different programs are actually using different > expressions for B3LYP, because of a lot of confusion about which VWN > functional was implied in the correlation part. Some codes use VWN5 (e.g. > TURBOMOLE, GAMESS and MOLPRO), whereas GAUSSIAN claims to be using VWN3 and > NWCHEM follows the GAUSSIAN definition. As a result B3LYP energies from > GAMESS and MOLPRO will differ from those obtained from GAUSSIAN and NWCHEM. > > Best wishes, > > Huub van Dam > CCLRC Daresbury Laboratory > h.j.j.vandam=at=dl.ac.uk From chemistry-request@ccl.net Tue Sep 23 15:53:58 2003 Received: from red.CACheSoftware.com ([12.17.172.66]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8NJrPmK018120 for ; Tue, 23 Sep 2003 15:53:25 -0400 Received: from DAVEG-LIFEBOOK.cachesoftware.com (netscreen.cachesoftware.com [12.17.172.74]) by red.CACheSoftware.com (8.11.6/8.9.3/3) with ESMTP id h8NJrQd31643; Tue, 23 Sep 2003 12:53:26 -0700 Message-Id: <5.2.1.1.0.20030923121856.02c97c68(at)mail.cachesoftware.com> X-Sender: daveg(at)mail.cachesoftware.com (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.2.1 Date: Tue, 23 Sep 2003 12:47:12 -0700 To: sergiusz.kwasniewski(at)luc.ac.be From: David Gallagher Subject: Re: CCL:reactivity and toxic level Cc: chemistry(at)ccl.net In-Reply-To: <1064296917.3f6fe1d51f05f(at)webmail.luc.ac.be> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_22996497==.ALT" X-Spam-Status: No, hits=0.5 required=7.0 tests=EMAIL_ATTRIBUTION,HTML_00_10,HTML_MESSAGE,IN_REP_TO, MIME_LONG_LINE_QP version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) --=====================_22996497==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Dear Serge, Fukui's indices, such as superdelocalizability, have been shown to correlate with biological activities and toxicities including carcinogenicity. Fukui's indices are derived by post-processing a QC calculation such as MOPAC. The whole process is automated in programs such as CAChe. It takes from a few seconds to a few minutes on a Windows machine to compute a range of indices including susceptibility to nucleophilic attack, susceptibility to electrophilic attack, susceptibility to radical attack, superdelocalizability, etc. for all atoms in the molecule. CAChe can then automatically regress all calculated descriptors against the experimental data to find the best correlation. The QSAR paper below used superdelocalizability to predict carcinogenicity. If you have trouble locating the paper, I may be able to find a reprint for you. *A Mechanism-mediated Model for Carcinogenicity, Rich Purdy (3M), Environmental Health Perspectives, 1085-94, Vol 104, Sup. 5, Oct. 1996 Regards, David Gallagher Fujitsu At 08:01 AM 9/23/2003 +0200, sergiusz.kwasniewski(at)luc.ac.be wrote: >Dear all, > >I wonder if there is any way to obtain information on the reactivity and the >toxic level of organic compounds by means of QC methods. I can imagine that >e.g. the internal charge distribution could give some insights into the >reactivity of the system (electron rich or poor). If possible a fast method, >which is reliable for organic compounds - both conjugated as not conjugated - >is prefered. Do you have any up-to-date reading in mind on this topic ? > >Please let me know. If wanted, I can make a summary. > >Dr. Serge Kwasniewski > > >-= This is automatically added to each message by the mailing script =- >To send e-mail to subscribers of CCL put the string CCL: on your Subject: line >and send your message to: CHEMISTRY(at)ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST(at)ccl.net >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >If your mail is bouncing from CCL.NET domain send it to the maintainer: >Jan Labanowski, jkl(at)ccl.net (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ --=====================_22996497==.ALT Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Serge,

Fukui's indices, such as superdelocalizability, have been shown to correlate with biological activities and toxicities including carcinogenicity. Fukui's indices are derived by post-processing a QC calculation such as MOPAC. The whole process is automated in programs such as CAChe. It takes from a few seconds to a few minutes on a Windows machine to compute a range of indices including susceptibility to nucleophilic attack, susceptibility to electrophilic attack, susceptibility to radical attack, superdelocalizability, etc. for all atoms in the molecule. CAChe can then automatically regress all calculated descriptors against the experimental data to find the best correlation. The QSAR paper below used superdelocalizability to predict carcinogenicity. If you have trouble locating the paper, I may be able to find a reprint for you.

*A Mechanism-mediated Model for Carcinogenicity, Rich Purdy (3M), Environmental Health Perspectives, 1085-94, Vol 104, Sup. 5, Oct. 1996

Regards,
David Gallagher
Fujitsu


At 08:01 AM 9/23/2003 +0200, sergiusz.kwasniewski(at)luc.ac.be wrote:
Dear all,

I wonder if there is any way to obtain information on the reactivity and the
toxic level of organic compounds by means of QC methods. I can imagine that
e.g. the internal charge distribution could give some insights into the
reactivity of the system (electron rich or poor). If possible a fast method,
which is reliable for organic compounds - both conjugated as not conjugated -
is prefered. Do you have any up-to-date reading in mind on this topic ?

Please let me know. If wanted, I can make a summary.

Dr. Serge Kwasniewski


-=3D This is automatically added to each message by the mailing script =3D-
To send e-mail to subscribers of CCL put the string CCL: on your Subject: line
and send your message to:  CHEMISTRY(at)ccl.net

Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST(at)ccl.net
HOME Page: http://www.ccl.net&= nbsp; | Jobs Page: http://www.ccl.net/jo= bs

If your mail is bouncing from CCL.NET domain send it to the maintainer:
Jan Labanowski,  jkl(at)ccl.net (read about it on CCL Home Page)
-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ --=====================_22996497==.ALT-- From chemistry-request@ccl.net Wed Sep 24 00:51:48 2003 Received: from front3.chartermi.net (front3.chartermi.net [24.213.60.109]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8O4phmK012721 for ; Wed, 24 Sep 2003 00:51:44 -0400 Received: from [24.236.135.230] (HELO master.bw01.kressworks.com) by front3.chartermi.net (CommuniGate Pro SMTP 3.5.9a) with ESMTP id 326730534 for chemistry(at)ccl.net; Wed, 24 Sep 2003 00:51:42 -0400 Content-Type: text/plain; charset="us-ascii" From: CCL To: chemistry(at)ccl.net Subject: Re: CCL:B3LYP functional specification of constants Date: Wed, 24 Sep 2003 00:44:33 +0000 User-Agent: KMail/1.4.3 MIME-Version: 1.0 Message-Id: <200309240044.33210.ccl(at)kressworks.com> X-Spam-Status: No, hits=3.3 required=7.0 tests=DATE_IN_PAST_03_06,QUOTED_EMAIL_TEXT,RCVD_IN_OSIRUSOFT_COM, USER_AGENT_KMAIL,X_OSIRU_OPEN_RELAY version=2.55 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h8O4pmmK012727 My original question: > While investigating prior to doing some extensive B3LYP calculations, I've > noticed that GAMESS and MOLPRO use 0.08 times the Slater Exchange in the > B3LYP functional while NWCHEM and GAUSSIAN use 0.8. Which is correct? Received one reply. Thanks to Huub van Dam for his response (given at the end of this note). In addition, from the GAMESS manual: > Note that B3LYP in GAMESS is based in part on the VWN5 > correlation functional. Since there are five formulae > in the VWN paper for local correlation, other programs > may use other formulae, and therefore generate different > B3LYP energies. For example, NWChem's manual says it uses > the "VWN 1 functional with RPA parameters as opposed to the > prescribed Monte Carlo parameters", but NWChem can be made > to use the VWN5 formula by > xc HFexch 0.20 slater 0.80 becke88 nonlocal 0.72 > lyp 0.81 vwn_5 0.19 > If you use some other program, its B3LYP energy will be > different from GAMESS if it does not employ VWN5. So we see there is no unique definition for the b3lyp functional. This seems a recipie for confusion but hey, what do I know? Note: MOLPRO and GAMESS (as of their current incarnations) use the same definition for the b3lyp functional. Jim > I think MOLPRO uses 0.8 times the Slater Exchange functional as well. The > confusion stems from what people call the Becke '88 functional. In MOLPRO > the Becke '88 functional is defined as > > B88 = rho^(4/3)*(c+dB88) > > where dB88 is the gradient enhancement factor and c*rho^(4/3) is the Slater > functional. In other codes the functional is defined as > > B88' = rho^(4/3)*dB88 > > without the Slater functional term. Of course the parameters you have to > use to arrive at the correct B3LYP expression depend on which definition of > the Becke '88 you use. > > A different matter is that different programs are actually using different > expressions for B3LYP, because of a lot of confusion about which VWN > functional was implied in the correlation part. Some codes use VWN5 (e.g. > TURBOMOLE, GAMESS and MOLPRO), whereas GAUSSIAN claims to be using VWN3 and > NWCHEM follows the GAUSSIAN definition. As a result B3LYP energies from > GAMESS and MOLPRO will differ from those obtained from GAUSSIAN and NWCHEM. > > Best wishes, > > Huub van Dam > CCLRC Daresbury Laboratory > h.j.j.vandam(at)dl.ac.uk From chemistry-request@ccl.net Tue Sep 23 23:22:48 2003 Received: from ns.cwp.co.kr ([210.109.76.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8O3MEmK006735 for ; Tue, 23 Sep 2003 23:22:16 -0400 Received: from cri2p ([172.24.15.92]) by ns.cwp.co.kr (8.9.3 (PHNE_25184)/8.9.3) with ESMTP id MAA03101 for ; Wed, 24 Sep 2003 12:18:52 +0900 (KST) From: "Sei-Hwan Kim" To: Subject: CCL: ab initio method of redical scavenger Date: Wed, 24 Sep 2003 12:22:02 +0900 Message-ID: <000001c3824b$075b5510$5c0f18ac@cri2p> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0001_01C38296.774483B0" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4925.2800 X-Spam-Status: No, hits=3.7 required=7.0 tests=HTML_COMMENT_8BITS,HTML_FONT_FACE_BAD,HTML_FONT_FACE_ODD, HTML_MESSAGE version=2.55 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ------=_NextPart_000_0001_01C38296.774483B0 Content-Type: text/plain; charset="ks_c_5601-1987" Content-Transfer-Encoding: quoted-printable Dear CCL readers=20 =20 Hi. CCLer ! =20 Would you give me the information of ab initio of radical scavenger? We will try to calculate the radical scavenger, but we can=A1=AFt find = the review or useful paper.=20 =20 Thanks! =20 Sean=20 =20 seihkim(at)cwp.co.kr ------=_NextPart_000_0001_01C38296.774483B0 Content-Type: text/html; charset="ks_c_5601-1987" Content-Transfer-Encoding: quoted-printable

Dear CCL readers =

 

Hi. CCLer !

 

Would you give me the information of ab initio of radical = scavenger?

We will try to calculate the radical = scavenger, but we can=A1=AFt find the = review or useful paper.

 

Thanks!

 

Sean

 

seihkim(at)cwp.co.kr

------=_NextPart_000_0001_01C38296.774483B0-- From chemistry-request@ccl.net Wed Sep 24 19:53:27 2003 Received: from mrelay2.inscc.utah.edu (mrelay2.inscc.utah.edu [155.101.3.58]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8ONqumK007407 for ; Wed, 24 Sep 2003 19:52:56 -0400 Received: from mail.inscc.utah.edu (mail.inscc.utah.edu [155.101.3.59]) by mrelay2.inscc.utah.edu (Postfix) with ESMTP id 0DFE81CE6B for ; Wed, 24 Sep 2003 19:52:56 -0400 (EDT) Received: from rydberg.hec.utah.edu (rydberg.hec.utah.edu [155.101.19.15]) by mail.inscc.utah.edu with ESMTP id RAA24119 for ; Wed, 24 Sep 2003 17:52:39 -0600 (MDT) Date: Wed, 24 Sep 2003 17:52:53 -0600 (MDT) From: Robert Gdanitz X-X-Sender: gdanitz.-at-.localhost.localdomain To: Computational Chemistry List Subject: Computational Chemistry on Macs Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) We plan to build a small workstation cluster, essentially for desktop work and some smaller computations over night. The system should be protected against power outages by a "smart" interruptible power supply (UPS) that initiates an automatic shut down when the batteries are emptied. Moreover, the system should be protected against data loss using a backup robot. The standard platforms in our field are nowadays probably Linux-PCs. However, due to reasons of support, I would like to use Apple Macs which now come with a Unix flavor as well. I would appreciate to hear about your experience/opinions on using the latest Macs (with Unix) in computational chemistry. I will summarize to the list. Thanks, Robert --- Robert J. Gdanitz Physics Dept., North Carolina A&T State University Marteena Hall, Rm. 101, Greensboro, NC 27411 Tel: (336) 334-7646 or -7647, Fax: (336) 256-0815 gdanitz.-at-.ncat.edu, http://gdanitz.hec.utah.edu From chemistry-request@ccl.net Wed Sep 24 19:01:08 2003 Received: from zephyr.meteo.McGill.CA (zephyr.Meteo.McGill.CA [132.206.43.13]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h8ON0bmK030962 for ; Wed, 24 Sep 2003 19:00:37 -0400 Received: from kinetic.Meteo.McGill.CA by zephyr.meteo.McGill.CA (AIX 4.1/UCB 5.64/4.03) id AA14456; Wed, 24 Sep 2003 19:00:33 -0400 Date: Wed, 24 Sep 2003 18:58:12 -0400 From: Andrew Ryzhkov X-Mailer: The Bat! (v1.61) Reply-To: Andrew Ryzhkov Organization: Dep. of Atm. & Oc. Sci. McGill Univ. X-Priority: 3 (Normal) Message-Id: <796767671.20030924185812.-at-.zephyr.meteo.mcgill.ca> To: chemistry.-at-.ccl.net Subject: Reaction rate and equilibrium constants calculation Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCLers, I have a bit stupid question: the reaction rate constant in the TS theory is calculated as k(T) = kBT/h exp(-deltaG#/(RT)). Inserting the deltaG# from my quantum chemistry calculation into this formula I get the rate constant in sec-1 units. But for a bimolecular reaction, the rate constant must be in L/(mol sec) or cm3/(molecule sec) units, not just 1/sec. Same thing for the equilibrium constant: K=exp(-deltaG/RT) is unitless not in the units of concentration. What is the way to get the rate and equilibrium constants in proper units? Best regards, Andrew Dr. Andrei Ryjkov Departments of Chemistry, and Atmospheric and Oceanic Sciences, McGill University, 805 Sherbrooke St. West #808 Montreal, Quebec, CANADA, H3A 2K6. -------------------------------------- Phone: +1(514)398-8867 Fax: +1(514)398-6115 -------------------------------------- E-mail: Andrew.-at-.Zephyr.Meteo.McGill.Ca Internet: http://RedAndr.tripod.com From chemistry-request@ccl.net Wed Sep 24 13:40:28 2003 Received: from red.CACheSoftware.com ([12.17.172.66]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8OHdumK002779; Wed, 24 Sep 2003 13:39:56 -0400 Received: from DAVEG-LIFEBOOK.cachesoftware.com (netscreen.cachesoftware.com [12.17.172.74]) by red.CACheSoftware.com (8.11.6/8.9.3/3) with ESMTP id h8OHf8d16912; Wed, 24 Sep 2003 10:41:08 -0700 Message-Id: <5.2.1.1.0.20030924102640.028ece00[at]mail.cachesoftware.com> X-Sender: daveg[at]mail.cachesoftware.com (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.2.1 Date: Wed, 24 Sep 2003 10:34:40 -0700 To: chemistry[at]ccl.net From: David Gallagher Subject: CCL:reactivity and toxic level Cc: chemistry-request[at]ccl.net Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_3948487==.ALT" X-Spam-Status: No, hits=1.3 required=7.0 tests=HTML_00_10,HTML_MESSAGE version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) --=====================_3948487==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed For those who have asked, there is an abstract and option to request Rich Purdy's carcinogenicity QSAR paper at the URL below. The author, Rich Purdy, can be reached at http://ehpnet1.niehs.nih.gov/docs/1996/Suppl-5/purdyabs.html Another reference that may be relevant: Purdy R. The utility of computed superdelocalizability for predicting the LC50 values of epoxides to guppies. Sci Total Environ 109/110:553-556 (1991) David Gallagher Fujitsu >Date: Tue, 23 Sep 2003 12:47:12 -0700 >To: sergiusz.kwasniewski[at]luc.ac.be >From: David Gallagher >Subject: CCL:reactivity and toxic level > >Dear Serge, > >Fukui's indices, such as superdelocalizability, have been shown to >correlate with biological activities and toxicities including >carcinogenicity. Fukui's indices are derived by post-processing a QC >calculation such as MOPAC. The whole process is automated in programs such >as CAChe. It takes from a few seconds to a few minutes on a Windows >machine to compute a range of indices including susceptibility to >nucleophilic attack, susceptibility to electrophilic attack, >susceptibility to radical attack, superdelocalizability, etc. for all >atoms in the molecule. CAChe can then automatically regress all calculated >descriptors against the experimental data to find the best correlation. >The QSAR paper below used superdelocalizability to predict >carcinogenicity. If you have trouble locating the paper, I may be able to >find a reprint for you. > >*A Mechanism-mediated Model for Carcinogenicity, Rich Purdy (3M), >Environmental Health Perspectives, 1085-94, Vol 104, Sup. 5, Oct. 1996 > >Regards, >David Gallagher >Fujitsu > > >At 08:01 AM 9/23/2003 +0200, sergiusz.kwasniewski[at]luc.ac.be wrote: >>Dear all, >> >>I wonder if there is any way to obtain information on the reactivity and the >>toxic level of organic compounds by means of QC methods. I can imagine that >>e.g. the internal charge distribution could give some insights into the >>reactivity of the system (electron rich or poor). If possible a fast method, >>which is reliable for organic compounds - both conjugated as not >>conjugated - >>is prefered. Do you have any up-to-date reading in mind on this topic ? >> >>Please let me know. If wanted, I can make a summary. >> >>Dr. Serge Kwasniewski >> --=====================_3948487==.ALT Content-Type: text/html; charset="us-ascii" For those who have asked, there is an abstract and option to request Rich Purdy's carcinogenicity QSAR paper at the URL below. The author, Rich Purdy, can be reached at <rpurdy[at]pressenter.com>

http://ehpnet1.niehs.nih.gov/docs/1996/Suppl-5/purdyabs.html

Another reference that may be relevant:
Purdy R. The utility of computed superdelocalizability for predicting the LC50 values of epoxides to guppies. Sci Total Environ 109/110:553-556 (1991)

David Gallagher
Fujitsu

Date: Tue, 23 Sep 2003 12:47:12 -0700
To: sergiusz.kwasniewski[at]luc.ac.be
From: David Gallagher <dgallagher[at]cachesoftware.com>
Subject: CCL:reactivity and toxic level

Dear Serge,

Fukui's indices, such as superdelocalizability, have been shown to correlate with biological activities and toxicities including carcinogenicity. Fukui's indices are derived by post-processing a QC calculation such as MOPAC. The whole process is automated in programs such as CAChe. It takes from a few seconds to a few minutes on a Windows machine to compute a range of indices including susceptibility to nucleophilic attack, susceptibility to electrophilic attack, susceptibility to radical attack, superdelocalizability, etc. for all atoms in the molecule. CAChe can then automatically regress all calculated descriptors against the experimental data to find the best correlation. The QSAR paper below used superdelocalizability to predict carcinogenicity. If you have trouble locating the paper, I may be able to find a reprint for you.

*A Mechanism-mediated Model for Carcinogenicity, Rich Purdy (3M), Environmental Health Perspectives, 1085-94, Vol 104, Sup. 5, Oct. 1996

Regards,
David Gallagher
Fujitsu


At 08:01 AM 9/23/2003 +0200, sergiusz.kwasniewski[at]luc.ac.be wrote:
Dear all,

I wonder if there is any way to obtain information on the reactivity and the
toxic level of organic compounds by means of QC methods. I can imagine that
e.g. the internal charge distribution could give some insights into the
reactivity of the system (electron rich or poor). If possible a fast method,
which is reliable for organic compounds - both conjugated as not conjugated -
is prefered. Do you have any up-to-date reading in mind on this topic ?

Please let me know. If wanted, I can make a summary.

Dr. Serge Kwasniewski

--=====================_3948487==.ALT-- From chemistry-request@ccl.net Wed Sep 24 12:34:41 2003 Received: from mail.salve.edu (mail.salve.edu [12.154.160.20]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8OGY9mK031713 for ; Wed, 24 Sep 2003 12:34:10 -0400 Received: from salve.edu ([12.154.160.74]) by mail.salve.edu (8.9.3 (MessagingDirect 1.0.4)/8.9.3) with SMTP id MAA08096 for ; Wed, 24 Sep 2003 12:50:02 -0400 Message-ID: <3F71C805.9E5B3783[at]salve.edu> Date: Wed, 24 Sep 2003 12:36:21 -0400 From: "Ascanio G. DiPippo" X-Mailer: Mozilla 4.7 [en] (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY[at]ccl.net Subject: CCL Mississippi Conference. Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-0.1 required=7.0 tests=X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Colleagues, Would someone be so kind as to send information or a link to the conference in Vucksburg this November. Thank you. Ascanio From chemistry-request@ccl.net Wed Sep 24 14:38:34 2003 Received: from p08.es.uci.edu (p08.es.uci.edu [128.200.73.148]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8OIc2mK009444 for ; Wed, 24 Sep 2003 14:38:03 -0400 Received: from 128.200.204.132 (dhcp-204132.bio.uci.edu [128.200.204.132]) by p08.es.uci.edu (8.11.6/8.11.6) with ESMTP id h8OIbx924639 for ; Wed, 24 Sep 2003 11:37:59 -0700 Date: Wed, 24 Sep 2003 11:37:58 -0700 From: Qiang Lu X-Mailer: The Bat! (v1.62r) Reply-To: Qiang Lu Organization: UCI MBB X-Priority: 3 (Normal) Message-ID: <1987484963.20030924113758_at_uci.edu> To: chemistry_at_ccl.net Subject: projection code MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi CCLers, I am working with AMBER7's projection of normal modes vibration and try to compare it with g03 to get force constant for AMBER.. I need to code of g03's projection of normal mode vibrations. The projection is project the vibration to internal coordinates. Our university has the g03's program but not code. -- Best regards, Qiang mailto:qiangl_at_uci.edu From chemistry-request@ccl.net Wed Sep 24 13:53:35 2003 Received: from periwinkle.noc.ucla.edu (periwinkle.noc.ucla.edu [169.232.47.11]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8OHr2mK003939 for ; Wed, 24 Sep 2003 13:53:02 -0400 Received: from orchid.noc.ucla.edu (orchid.noc.ucla.edu [169.232.48.12]) by periwinkle.noc.ucla.edu (8.12.8p2/8.12.8) with ESMTP id h8OHqwuN005979; Wed, 24 Sep 2003 10:52:58 -0700 Received: from dsievers (Dsievers.seas.ucla.edu [128.97.82.155]) (authenticated bits=0) by orchid.noc.ucla.edu (8.12.9p1/8.12.9) with ESMTP id h8OHqvOQ021006 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT); Wed, 24 Sep 2003 10:52:57 -0700 Message-ID: <003d01c382c4$abc15180$9b526180:at:seas.ucla.edu> From: "Douglas Sievers" To: Cc: References: <200309240044.33210.ccl:at:kressworks.com> Subject: Re: B3LYP functional specification of constants Date: Wed, 24 Sep 2003 10:52:48 -0700 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 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Scanned-By: MIMEDefang 2.25 / SpamAssassin 2.43 / mail.ucla.edu X-Probable-Spam: no X-Spam-Hits: -0.3 X-Spam-Status: No, hits=-1.0 required=7.0 tests=QUOTED_EMAIL_TEXT,REFERENCES version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Jim, In one of my reference books I was pointed to a journal article that explains what parameters are used for each functional and attempts to rationalize the selection of those parameters. The discussion uses Gaussian92 for implementation. Here is the reference. P. J. Stephens, F. J. Devlin, C. F. Chabalowski, and M. J. Frisch, "Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields," J. Phys. Chem. 98, pp 11623 - 11627 (1994). To put it briefly, I believe 0.8 is correct, but be careful. There is some confusion because the B3LYP functional is described as (giving only first 2 terms) Exc(B3LYP) = (1-a)*Ex(LSDA) + a*Ex(HF) + . . . The value used for a=0.2, which would mean that only 0.2 times the Slater exchange is included and 0.8 is due to the LSDA approximation. I recommend reading the journal article above to make it clear. Douglas Sievers Graduate Student Researcher UCLA Materials Sci & Eng 3049 Engineering 1 (310) 794-6491 dsievers:at:ucla.edu ----- Original Message ----- From: "CCL" To: Sent: Tuesday, September 23, 2003 5:44 PM Subject: CCL:B3LYP functional specification of constants > My original question: > > > While investigating prior to doing some extensive B3LYP calculations, I've > > noticed that GAMESS and MOLPRO use 0.08 times the Slater Exchange in the > > B3LYP functional while NWCHEM and GAUSSIAN use 0.8. Which is correct? > > Received one reply. Thanks to Huub van Dam for his response (given at the end > of this note). In addition, from the GAMESS manual: > > > Note that B3LYP in GAMESS is based in part on the VWN5 > > correlation functional. Since there are five formulae > > in the VWN paper for local correlation, other programs > > may use other formulae, and therefore generate different > > B3LYP energies. For example, NWChem's manual says it uses > > the "VWN 1 functional with RPA parameters as opposed to the > > prescribed Monte Carlo parameters", but NWChem can be made > > to use the VWN5 formula by > > xc HFexch 0.20 slater 0.80 becke88 nonlocal 0.72 > > lyp 0.81 vwn_5 0.19 > > If you use some other program, its B3LYP energy will be > > different from GAMESS if it does not employ VWN5. > > So we see there is no unique definition for the b3lyp functional. This seems > a recipie for confusion but hey, what do I know? > > Note: MOLPRO and GAMESS (as of their current incarnations) use the same > definition for the b3lyp functional. > > Jim > > > > I think MOLPRO uses 0.8 times the Slater Exchange functional as well. The > > confusion stems from what people call the Becke '88 functional. In MOLPRO > > the Becke '88 functional is defined as > > > > B88 = rho^(4/3)*(c+dB88) > > > > where dB88 is the gradient enhancement factor and c*rho^(4/3) is the Slater > > functional. In other codes the functional is defined as > > > > B88' = rho^(4/3)*dB88 > > > > without the Slater functional term. Of course the parameters you have to > > use to arrive at the correct B3LYP expression depend on which definition of > > the Becke '88 you use. > > > > A different matter is that different programs are actually using different > > expressions for B3LYP, because of a lot of confusion about which VWN > > functional was implied in the correlation part. Some codes use VWN5 (e.g. > > TURBOMOLE, GAMESS and MOLPRO), whereas GAUSSIAN claims to be using VWN3 and > > NWCHEM follows the GAUSSIAN definition. As a result B3LYP energies from > > GAMESS and MOLPRO will differ from those obtained from GAUSSIAN and NWCHEM. > > > > Best wishes, > > > > Huub van Dam > > CCLRC Daresbury Laboratory > > h.j.j.vandam:at:dl.ac.uk > > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY:at:ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST:at:ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl:at:ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > From chemistry-request@ccl.net Wed Sep 24 10:23:52 2003 Received: from emily.fle.fujitsu.com ([193.122.18.249]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h8OENKmK032659 for ; Wed, 24 Sep 2003 10:23:21 -0400 Received: by fle2.fle.fujitsu.com with Internet Mail Service (5.5.2656.59) id ; Wed, 24 Sep 2003 15:12:50 +0100 Message-ID: From: h.fruchtl:at:fle.fujitsu.com To: jimkress:at:kressworks.com, chemistry:at:ccl.net Subject: CCL: RE: B3LYP functional specification of constants Date: Wed, 24 Sep 2003 15:12:45 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2656.59) Content-Type: multipart/mixed; boundary="----=_NextPartTM-000-a1ddc4c4-cfec-423d-8afc-8726e02350ea" X-Spam-Status: No, hits=0.7 required=7.0 tests=MIME_BOUND_NEXTPART,NO_REAL_NAME,QUOTED_EMAIL_TEXT version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ------=_NextPartTM-000-a1ddc4c4-cfec-423d-8afc-8726e02350ea Content-Type: text/plain > > So we see there is no unique definition for the b3lyp functional. > This seems > a recipie for confusion but hey, what do I know? > I remember this discussion from some time ago. The argument of those who implemented the Gaussian version was that Gaussian invented and named it, so B3LYP should refer to how Gaussian did it, and not to how it should have been done. Scientifically, the improved versions should be "better" (in that vague sense of the word as you have to use it wrt functionals). But this is > from memory, and I'm not claiming to correctly represent anybody else's opinions. Herbert ------=_NextPartTM-000-a1ddc4c4-cfec-423d-8afc-8726e02350ea Content-Type: text/plain; name="InterScan_Disclaimer.txt" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="InterScan_Disclaimer.txt" This e-mail has been scanned by Trend InterScan Software. This e-mail (and its attachment(s) if any) is intended for the named addressee(s) only. It may contain information which is privileged and confidential within the meaning of the applicable law. Unauthorised use, copying or disclosure is strictly prohibited and may be unlawful. If you are not the intended recipient please delete this email and contact the sender via email return. Fujitsu Laboratories of Europe Ltd (FLE) does not accept responsibility for changes made to this email after it was sent. The views expressed in this email may not necessarily be the views held by FLE. Unless expressly stated otherwise, this email does not form part of a legally binding contract or agreement between the recipient and Fujitsu Laboratories of Europe Ltd (FLE). ------=_NextPartTM-000-a1ddc4c4-cfec-423d-8afc-8726e02350ea--