From owner-chemistry@ccl.net Mon Jun 26 00:36:00 2006 From: "Green Power powergreen^-^gmail.com" To: CCL Subject: CCL: SQM Message-Id: <-32008-060624135833-4600-oJDNZm1yIwwxLvXxTR0HOA . server.ccl.net> X-Original-From: "Green Power" Content-Type: multipart/alternative; boundary="----=_Part_37086_8132513.1151168271950" Date: Sat, 24 Jun 2006 12:57:51 -0400 MIME-Version: 1.0 Sent to CCL by: "Green Power" [powergreen[A]gmail.com] ------=_Part_37086_8132513.1151168271950 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi, Anybody know what kind of program should be used to do SQM (Scaled Quantum Mechanical) vibration calculation? Your help is appreciated. ------=_Part_37086_8132513.1151168271950 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hi,
 
Anybody know what kind of program should be used to do SQM (Scaled Quantum Mechanical) vibration calculation?
Your help is appreciated.
 
------=_Part_37086_8132513.1151168271950-- From owner-chemistry@ccl.net Mon Jun 26 01:28:01 2006 From: "Dr. Sudhir A. Kulkarni sudhirk(_)vlifesciences.com" To: CCL Subject: CCL: Schwartz-like inequality on Coulomb and exchange integrals Message-Id: <-32009-060626011625-718-xvv5JyBnFTLHgcCe4VRfCQ-*-server.ccl.net> X-Original-From: "Dr. Sudhir A. Kulkarni" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 26 Jun 2006 10:08:19 +0530 MIME-Version: 1.0 Sent to CCL by: "Dr. Sudhir A. Kulkarni" [sudhirk(a)vlifesciences.com] Igor, Look at following papers. Rigorous bounds to molecular electron repulsion and electro-static potential integrals: S.R. Gadre, S.A. Kulkarni, R.K. Pathak J. Chem. Phys. 91, 3596-3602 (1989). Some aspects of parallelization of two-electron integrals in molecular orbital programs S.R. Gadre, S.A. Kulkarni, A.C. Limaye, R.N. Shirsat Z. Phys.D-Atoms, Molecules and Clusters 18, 357-363 (1991) If you don't get these papers yourself write a request to Professor Gadre at gadre++chem.unipune.ernet.in Hope this is useful. Regards. Sudhir Igor Schweigert ischweig-.-uci.edu wrote: >Sent to CCL by: "Igor Schweigert" [ischweig[a]uci.edu] >------=_Part_26477_20075059.1151085235334 >Content-Type: text/plain; charset=ISO-8859-1; format=flowed >Content-Transfer-Encoding: 7bit >Content-Disposition: inline > >Hi, > >I wonder if someone knows a reference to a discussion of the inequality >between the Coulomb- and exchange-type ERI of two basis functions : > >(ij|ji) <= (ii|jj) (Mulliken notation) > >I know I've seen it discussed somewhere but cannot recall where. I've tried >Web of Science and Google Scholar searches but to no avail (most matches >lead to the Schwartz condition on the four-index ERI). > >Thanks in advance, >Igor > >------=_Part_26477_20075059.1151085235334 >Content-Type: text/html; charset=ISO-8859-1 >Content-Transfer-Encoding: 7bit >Content-Disposition: inline > >Hi,
>
>I wonder if someone knows a reference to a discussion of >the inequality between the Coulomb- and exchange-type ERI of two basis >functions :
>
>(ij|ji) <= (ii|jj)  (Mulliken notation)
>
>I know I've seen it discussed somewhere but >cannot recall where. I've tried Web of Science and Google Scholar >searches but to no avail (most matches lead to the Schwartz condition on the four-index ERI).
>
>Thanks in advance,
>Igor
>
>
>
> >------=_Part_26477_20075059.1151085235334--> > > > > > -- Sudhir A. Kulkarni, Ph.D. VLife Sciences Technologies Pvt. Ltd. 1 Akshay, 50 Anand Park Aundh, Pune 411007 INDIA Tel: +91-20-2588-6737 ---------------------------------------------------------------------------------------------------------------------------------------- VLife Sciences Technologies Pvt Ltd.(VLife); Mail Disclaimer: This e-mail and any files transmitted with it are confidential and the views expressed in the same are not necessarily the views of VLife, and its Directors, Management, Employees or Associates. This communication represents the originator's personal views and opinions. If you are not the intended recipient or the person responsible for delivering the e-mail to the intended recipient, be advised that you have received this e-mail by error, and that any use, dissemination, forwarding, printing, or copying of this e-mail is strictly prohibited. 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The rights to monitor all e-mail communication through our network are reserved with us. ---------------------------------------------------------------------------------------------------------------------------------------- From owner-chemistry@ccl.net Mon Jun 26 03:31:01 2006 From: "Alfred Gil agil^cesca.es" To: CCL Subject: CCL:G: Laplacian plot of the electron density Message-Id: <-32010-060626032212-5982-A0j8IPdtf77aatQwlCZ01w(!)server.ccl.net> X-Original-From: Alfred Gil Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 26 Jun 2006 08:44:52 +0200 MIME-Version: 1.0 Sent to CCL by: Alfred Gil [agil===cesca.es] Hi, You can find FLOPO with its GUI Xaim, in next address: http://www.quimica.urv.es/%7Ew3qf/ It is a program developed in the Dept. of Physical Chemistry at University Rovira i Virgili (Tarragona, Spain), and it is distributed in binary form free of charge. Enjoy it! -- ...................................................................... __ / / Alfred Gil i Arranz C E / S / C A Departament de Sistemes /_/ Centre de Supercomputació de Catalunya Gran Capità, 2-4 (Edifici Nexus) · 08034 Barcelona T. 93 205 6464 · F. 93 205 6979 · agil##cesca.es ...................................................................... En/na S Lam chsue2004|,|yahoo.com ha escrit: > Sent to CCL by: "S Lam" [chsue2004- -yahoo.com] > Hi, > > Is there any free program can display the Laplacian of the electron density from the gaussian output? > > Thanks, > S Lam> > > > > > From owner-chemistry@ccl.net Mon Jun 26 04:06:01 2006 From: "Orlin Blajiev blajiev**vub.ac.be" To: CCL Subject: CCL:G: DipoleDeriv Message-Id: <-32011-060626033508-11496-k9O1BPVCf1+lObylc3KCPg]^[server.ccl.net> X-Original-From: Orlin Blajiev Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 26 Jun 2006 09:35:18 +0200 MIME-Version: 1.0 Sent to CCL by: Orlin Blajiev [blajiev##vub.ac.be] Hi, I just want to briefly summarize what I have been explained about this. 1. Gaussian outputs Input and Standard geometry. 2. At the end of the run there is as usual an archive entry and the components of the DipDeriv are given as rotated back to the INPUT orientation (the FIRST one or the OPTIMIZED one I do not know, but should be the optimized). 3. In order to have the components of the Dipole Derivatives in Standard orientation the instruction IOP(7/33=1) should be present. Then they appear in the form Dipole derivatives wrt mode 1: 5.01266D-01 -1.87527D-02 -4.66685D-09 Vibrational polarizability contributions from mode 1 0.3823903 Here follows the copy of the message from Gaussian about this question. "The data in the archive entry at the end of a Gaussian output is mostly in atomic units, structure being the main exception, and it is given in input orientation. So if you compare against the Dipole derivative in the formatted checkpoint file it is generally just rotated back into the input orientation. Generally I recommend getting all of the data from the formatted checkpoint file rather than the output because the formatted checkpoint file is all in standard orientation and atomic units." Best regards, Orlin -- Orlin Blajiev Department of Metallurgy, Electrochemistry and Materials Science Faculty of Applied Science Vrije Universiteit Brussel Pleinlaan 2, B-1050 Brussels Belgium http://www.vub.ac.be/META/ tel.: 32-(0)2-6293538 fax : 32-(0)2-6293200 From owner-chemistry@ccl.net Mon Jun 26 05:17:01 2006 From: "Rafael R. Pappalardo rafapa .. us.es" To: CCL Subject: CCL: SQM Message-Id: <-32012-060626043319-8767-cgfmENv67ypODjQzet08IA++server.ccl.net> X-Original-From: "Rafael R. Pappalardo" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 26 Jun 2006 09:33:04 +0200 MIME-Version: 1.0 Sent to CCL by: "Rafael R. Pappalardo" [rafapa()us.es] On Monday 26 June 2006 06:43, Green Power powergreen^-^gmail.com wrote: > Sent to CCL by: "Green Power" [powergreen[A]gmail.com] > > > ------=_Part_37086_8132513.1151168271950 > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > Content-Transfer-Encoding: 7bit > Content-Disposition: inline > > Hi, > > Anybody know what kind of program should be used to do SQM (Scaled Quantum > Mechanical) vibration calculation? > Your help is appreciated. > You could try http://www.pqs-chem.com they sell an sqm code for $50 (Academic). Best regards -- Dr. Rafael R. Pappalardo Dept. Physical Chemistry, Univ. de Sevilla (Spain) e-mail: rafapa-#-us.es From owner-chemistry@ccl.net Mon Jun 26 07:34:00 2006 From: "Pierre Archirel pierre.archirel|-|lcp.u-psud.fr" To: CCL Subject: CCL: answer to why Kij <= Jij ? Message-Id: <-32013-060626065946-1080-ZC30RqnCW/yWeEezLTlCMg/./server.ccl.net> X-Original-From: Pierre Archirel Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 26 Jun 2006 12:07:12 +0200 MIME-Version: 1.0 Sent to CCL by: Pierre Archirel [pierre.archirel!A!lcp.u-psud.fr] This is an answer to I. Schweigert. I find the following reasoning in the lecture, I had in the past from G. Bessis: 1- set a_ij=f_i(1).f_j(2).r_12**(-1/2), then J_ij = and K_ij = where p(ij) is the transposition operator for i and j. 2- prove that the mean value of a transposition is ruled by: -1 <= <= +1 (use T_ij=1/2(1-p_ij), prove it is idempotent and positive defined, also use 1-T in the same way) 3- this implies <= and eventually proves the statement. Best wishes P.A. __________________________________________________________ Pierre Archirel Groupe de Chimie Théorique Laboratoire de Chimie Physique Tel: 01 69 15 63 86 Bat 349 Fax: 01 69 15 61 88 91405 Orsay Cedex France pierre.archirel!A!lcp.u-psud.fr __________________________________________________________ From owner-chemistry@ccl.net Mon Jun 26 09:34:00 2006 From: "Rafal Korlacki rafal.korlacki\a/uni-tuebingen.de" To: CCL Subject: CCL: SQM Message-Id: <-32014-060626035323-22842-PfkhTbAtwIz5NqbE9j6DVw**server.ccl.net> X-Original-From: "Rafal Korlacki" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Mon, 26 Jun 2006 08:41:38 +0200 MIME-Version: 1.0 Sent to CCL by: "Rafal Korlacki" [rafal.korlacki|-|uni-tuebingen.de] There is an SQM application from Parallel Quantum Solutions (www.pqs-chem.com). Works fine. Regards, RK ----- Original Message ----- > From: "Green Power powergreen^-^gmail.com" To: "Korlacki, Rafal " Sent: Monday, June 26, 2006 7:00 AM Subject: CCL: SQM > Sent to CCL by: "Green Power" [powergreen[A]gmail.com] > > > Hi, > > Anybody know what kind of program should be used to do SQM (Scaled Quantum > Mechanical) vibration calculation? > Your help is appreciated. > From owner-chemistry@ccl.net Mon Jun 26 12:19:00 2006 From: "Igor Schweigert ischweig()uci.edu" To: CCL Subject: CCL: Schwartz-like inequality on Coulomb and exchange integrals Message-Id: <-32015-060626121551-25912-qkiEDHrzjA25aWLFjFIheA-$-server.ccl.net> X-Original-From: "Igor Schweigert" Content-Type: multipart/alternative; boundary="----=_Part_52888_13036860.1151338546353" Date: Mon, 26 Jun 2006 09:15:46 -0700 MIME-Version: 1.0 Sent to CCL by: "Igor Schweigert" [ischweig~!~uci.edu] ------=_Part_52888_13036860.1151338546353 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Sudhir, Thank you for the references, I have looked up the JCP and truly enjoyed reading it as it may give me a lead towards other issues I had. I need to spend more time following the references therein. Igor On 6/25/06, Dr. Sudhir A. Kulkarni sudhirk(_)vlifesciences.com < owner-chemistry:+:ccl.net> wrote: > > Sent to CCL by: "Dr. Sudhir A. Kulkarni" [sudhirk(a)vlifesciences.com] > Igor, > > Look at following papers. > Rigorous bounds to molecular electron repulsion and electro-static > potential integrals: > S.R. Gadre, S.A. Kulkarni, R.K. Pathak J. Chem. Phys. 91, 3596-3602 > (1989). > > Some aspects of parallelization of two-electron integrals in molecular > orbital programs > S.R. Gadre, S.A. Kulkarni, A.C. Limaye, R.N. Shirsat Z. Phys.D-Atoms, > Molecules and Clusters 18, 357-363 (1991) > > If you don't get these papers yourself write a request to Professor Gadre > at > gadre,+,chem.unipune.ernet.in > > Hope this is useful. > Regards. > > Sudhir > > ------=_Part_52888_13036860.1151338546353 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Sudhir,

Thank you for the references, I have looked up the JCP and truly enjoyed reading it as it may give me a lead towards other issues I had. I need to spend more time following the references therein.

Igor

On 6/25/06, Dr. Sudhir A. Kulkarni sudhirk(_)vlifesciences.com <owner-chemistry:+:ccl.net> wrote:
Sent to CCL by: "Dr. Sudhir A. Kulkarni" [sudhirk(a)vlifesciences.com]
Igor,

Look at following papers.
Rigorous bounds to molecular electron repulsion and electro-static
potential integrals:
S.R. Gadre, S.A. Kulkarni, R.K. Pathak J. Chem. Phys. 91, 3596-3602 (1989).

Some aspects of parallelization of two-electron integrals in molecular
orbital programs
S.R. Gadre, S.A. Kulkarni, A.C. Limaye, R.N. Shirsat Z. Phys.D-Atoms,
Molecules and Clusters 18, 357-363 (1991)

If you don't get these papers yourself write a request to Professor Gadre at
gadre,+,chem.unipune.ernet.in

Hope this is useful.
Regards.

Sudhir


------=_Part_52888_13036860.1151338546353-- From owner-chemistry@ccl.net Mon Jun 26 13:07:00 2006 From: "Chris Moth chris.moth###Vanderbilt.Edu" To: CCL Subject: CCL:G: Laplacian plot of the electron density Message-Id: <-32016-060624155142-15972-6Aij6kS3+Y0QsxPWtbNYcg/a\server.ccl.net> X-Original-From: "Chris Moth" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Sat, 24 Jun 2006 14:04:58 -0500 (CDT) MIME-Version: 1.0 Sent to CCL by: "Chris Moth" [chris.moth===Vanderbilt.Edu] Preston Macdougall did some interesting work in Laplacian visualization a few years ago - it resulted in mention in "Nature". You might contact him to see if this was ever released as "a package". I think he was considering doing this a few years ago, when I last spoke with him briefly about this. Check out: http://honors.web.mtsu.edu/macdougall1.htm > Sent to CCL by: "S Lam" [chsue2004- -yahoo.com] > Hi, > > Is there any free program can display the Laplacian of the electron > density from the gaussian output? > > Thanks, > S Lam ----------------------------------------------------------------- Chris Moth Vanderbilt University Email: christopher.moth^Vanderbilt.Edu From owner-chemistry@ccl.net Mon Jun 26 20:21:00 2006 From: "samuel.flores\a/yale.edu" To: CCL Subject: CCL: setting maxatm > 10,000 in tinker? Message-Id: <-32017-060626201933-26901-vS6wvg2lmmd8TdzBoFhOgw:server.ccl.net> X-Original-From: samuel.flores###yale.edu Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format="flowed" Date: Mon, 26 Jun 2006 20:19:23 -0400 MIME-Version: 1.0 Sent to CCL by: samuel.flores#,#yale.edu Hi Guys, I am trying to use the tinker pdbxyz, xyzpdb, minimize, and analyze commands on structures that when hydrogenated have more than 10,000 atoms. sizes.i has the parameter maxatm=10,000 by default. Increasing this number and recompiling results in non-working executables. I believe what I really need to do is increase maxatm and subsequently compile for 64-bit processors, which I posess. I think the 10,000 is an array size limitation for 32 bit processors. However I have no idea if recompiling for 64 bit will result in viable executables with maxatm > 10,000, or what the right flags are for g77. Any help with this is much appreciated. Sam From owner-chemistry@ccl.net Mon Jun 26 22:51:01 2006 From: "Sue Lam chsue2004() yahoo.com" To: CCL Subject: CCL:G: Laplacian plot of the electron density Message-Id: <-32018-060626224820-1569-URBrw1KF/OROkt16EolfrQ.@.server.ccl.net> X-Original-From: Sue Lam Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-278494486-1151376491=:21990" Date: Mon, 26 Jun 2006 19:48:11 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Sue Lam [chsue2004!A!yahoo.com] --0-278494486-1151376491=:21990 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear all, Thank you for your advice. S Lam "Chris Moth chris.moth###Vanderbilt.Edu" wrote: Sent to CCL by: "Chris Moth" [chris.moth===Vanderbilt.Edu] Preston Macdougall did some interesting work in Laplacian visualization a few years ago - it resulted in mention in "Nature". You might contact him to see if this was ever released as "a package". I think he was considering doing this a few years ago, when I last spoke with him briefly about this. Check out: http://honors.web.mtsu.edu/macdougall1.htm > Sent to CCL by: "S Lam" [chsue2004- -yahoo.com] > Hi, > > Is there any free program can display the Laplacian of the electron > density from the gaussian output? > > Thanks, > S Lam ----------------------------------------------------------------- Chris Moth Vanderbilt University Email: christopher.moth|a|Vanderbilt.Eduhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--------------------------------- How low will we go? Check out Yahoo! Messenger’s low PC-to-Phone call rates. --0-278494486-1151376491=:21990 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Dear all,
 
Thank you for your advice.
 
S Lam
 
 


"Chris Moth chris.moth###Vanderbilt.Edu" <owner-chemistry!^!ccl.net> wrote:
Sent to CCL by: "Chris Moth" [chris.moth===Vanderbilt.Edu]


Preston Macdougall did some interesting work in Laplacian visualization a
few years ago - it resulted in mention in "Nature". You might contact him
to see if this was ever released as "a package". I think he was
considering doing this a few years ago, when I last spoke with him briefly
about this.

Check out:

http://honors.web.mtsu.edu/macdougall1.htm


> Sent to CCL by: "S Lam" [chsue2004- -yahoo.com]
> Hi,
>
> Is there any free program can display the Laplacian of the electron
> density from the gaussian output?
>
> Thanks,
> S Lam

-----------------------------------------------------------------
Chris Moth
Vanderbilt University
Email: christopher.moth|a|Vanderbilt.Edu


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How low will we go? Check out Yahoo! Messenger’s low PC-to-Phone call rates. --0-278494486-1151376491=:21990--