From owner-chemistry@ccl.net Tue Nov 7 01:24:01 2006 From: "Silviu Polosan polosan+/-cc.kyoto-su.ac.jp" To: CCL Subject: CCL:G: ECP Message-Id: <-32947-061106212029-27162-aGysaQOCyA0HDksXHJj4Xw=server.ccl.net> X-Original-From: "Silviu Polosan" Date: Mon, 6 Nov 2006 21:20:28 -0500 Sent to CCL by: "Silviu Polosan" [polosan]*[cc.kyoto-su.ac.jp] Hello, Can anyone tell me how to include ECP in Gaussian03W calculations? Someone told me to use LANL2DZ functions, but I am affraid is not enought. Any answer will be appreciated. Thank you From owner-chemistry@ccl.net Tue Nov 7 03:05:00 2006 From: "alberto savoini alberto.savoini ~~ polimerieuropa.com" To: CCL Subject: CCL:G: problem wirh g03 D.02 Message-Id: <-32948-061106110756-29382-NeQIb8d8KiOmVWamoCgNHw#server.ccl.net> X-Original-From: "alberto savoini" Date: Mon, 6 Nov 2006 11:07:55 -0500 Sent to CCL by: "alberto savoini" [alberto.savoini(a)polimerieuropa.com] I've installed the upgrade for Gaussian ( g03 D.02 s/n FC8441343010) and LINDA ( Rev 7.1 s/n FC8341343020 ). My cluster has fedora core 3 and PGI 6.1. While the compilation is OK I have a problem running parallel jobs (%NProcShared=2 %NProcLinda=2) : setenv GAUSS_EXEDIR /opt2/g03d02/g03/linda-exe:/opt2/g03d02/g03/bsd:/opt2/g03d02/g03/local:/opt2/g03d02/g03/extras:/opt2/g03d02/g03 g03 test004.com Incorrectly built binary which accesses errno or h_errno directly. Needs to be fixed. ntsnet: using executable file /opt2/g03d02/g03/linda-exe/l302.exel ntsnet: trying to schedule 1 worker ntsnet: scheduled a total of 1 worker ntsnet: starting master process on node11.cluster ntsnet: starting 1 worker on node12.cluster l302.exel: machine.c:365: _l_md_post_local_recv: Assertion `!local_recv_sanity' failed. eval server 0 on node11.cluster has dropped it's connection. If I run a job using only one node ( 2 CPU ) it works correctly. Alberto Savoini - Sistemi Informativi Eni S.p.A. - Divisione Refining & Marketing Centro Ricerche di Novara - Istituto Guido Donegani Via Fauser,4 28100 Novara (NO) - Italy Tel. +39 0321 447505 Fax +39 0321 447679 email: alberto.savoini=polimerieuropa.com From owner-chemistry@ccl.net Tue Nov 7 05:24:00 2006 From: "Barbara Jagoda-Cwiklik barbara.cwiklik_+_uochb.cas.cz" To: CCL Subject: CCL:G: ECP Message-Id: <-32949-061107045817-22125-DtAmMLLO0lDDc3/R3Evatg*o*server.ccl.net> X-Original-From: "Barbara Jagoda-Cwiklik" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 7 Nov 2006 10:58:08 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: "Barbara Jagoda-Cwiklik" [barbara.cwiklik#%#uochb.cas.cz] > Sent to CCL by: "Silviu Polosan" [polosan]*[cc.kyoto-su.ac.jp] > Hello, > > Can anyone tell me how to include ECP in Gaussian03W calculations? Someone told me to use LANL2DZ functions, but I am affraid is not enought. > Any answer will be appreciated. Hi Silviu, If you have ECP that you need just use keyword Gen and than keyword Pseudo - I guess Gaussian Manual can be useful. Also go through some last replays by Kirk Peterson. Regards, Basia -- Barbara Jagoda-Cwiklik, Ph.D Center for Biomolecules and Complex Molecular Systems Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic Prague, Czech Republic e-mail: barbara.cwiklik .. uochb.cas.cz From owner-chemistry@ccl.net Tue Nov 7 05:59:00 2006 From: "Dipankar Roy dipankarroy(!)iitb.ac.in" To: CCL Subject: CCL:G: ECP Message-Id: <-32950-061107045636-21915-gsdV3XHebrPatZRHza6LGw!A!server.ccl.net> X-Original-From: "Dipankar Roy" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 7 Nov 2006 14:26:21 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: "Dipankar Roy" [dipankarroy[#]iitb.ac.in] Hi, Ckeck the link: http://www.gaussian.com/g_ur/k_pseudo.htm hope this will answer your question. -Dipankar Roy > Sent to CCL by: "Silviu Polosan" [polosan]*[cc.kyoto-su.ac.jp] > Hello, > > Can anyone tell me how to include ECP in Gaussian03W calculations? > Someone told me to use LANL2DZ functions, but I am affraid is not enought. > Any answer will be appreciated. > > Thank you> > > > *********************************************** Dipankar Roy Graduate Student of Prof. R. B. Sunoj Computational Chemistry Laboratory Dept. of Chemistry Indian Institute of Technology, Bombay India - 400076 Phone: +91-22-2576-4130(lab) URL: http://www.geocities.com/dipankar_roy79/dipankar.html *********************************************** GETTING A SIMPLE ANSWER FROM A PROFESSOR IS LIKE GETTING A THIMBLE OF WATER FROM A FIRE HYDRANT. - PROF. LEN SHAPIRO, NDSU From owner-chemistry@ccl.net Tue Nov 7 09:08:00 2006 From: "Filipe Duarte duarte|-|staff.uni-marburg.de" To: CCL Subject: CCL: Dipole moment - TDDFT Message-Id: <-32951-061106082441-28792-dSTmc4k7q7/tZkHuJp78Ew-,-server.ccl.net> X-Original-From: "Filipe Duarte" Date: Mon, 6 Nov 2006 08:24:40 -0500 Sent to CCL by: "Filipe Duarte" [duarte(a)staff.uni-marburg.de] Dear CClers I would like to ask a question about how to calculate dipole moments in excited stat using TDDFT. I would greatly appreciate it if anyone would kindly answer, comment, or address about this issue clearly. Thank you very much for your time. Best wishes, Filipe Duarte, Ph.D Fachbereich Chemie Philipps-Universitt Marburg Germany Email: duarte**staff.uni-marburg.de From owner-chemistry@ccl.net Tue Nov 7 11:34:01 2006 From: "Jimmy Lawrence jlawrence\a/slb.com" To: CCL Subject: CCL:G: Question about zeolite adsoption Message-Id: <-32952-061107070745-18019-j8ppfD0XmOM3I47Sop+tSQ**server.ccl.net> X-Original-From: Jimmy Lawrence Content-transfer-encoding: 7BIT Content-type: text/plain; charset=iso-2022-jp Date: Tue, 07 Nov 2006 20:12:33 +0900 MIME-version: 1.0 Sent to CCL by: Jimmy Lawrence [jlawrence^slb.com] Can anyone share their experiences on calculating gas molecules adsoption on zeolites using recent free/ commercial QM/MD softwares ? (such as Gaussian03, Materials Studio, Spartan, etc) I am interested in purchasing software that can give me qualitative interpretation of gas molecules diffusion inside the zeolite cage, can you share your experiences/recommendation ? Btw, personally QMD program looks very interesting, however I have no experiences on using it. It would be helpful if any of you can give advices about this, since being a Linux beginner, I prefer Windows system. Regards, -------------------------------------- Jimmy Lawrence JAPAN -------------------------------------- From owner-chemistry@ccl.net Tue Nov 7 12:09:00 2006 From: "Caroline Norris cn29---sussex.ac.uk" To: CCL Subject: CCL: Excited state electronic configurations Message-Id: <-32953-061107092819-17942-+m1ecpn6xlSAAH9JpGHqwA[a]server.ccl.net> X-Original-From: "Caroline Norris" Date: Tue, 7 Nov 2006 09:28:18 -0500 Sent to CCL by: "Caroline Norris" [cn29::sussex.ac.uk] Dear All, I am in the process of calculating the potential energy curves of the lowest lying excited state of neutral vanadium oxide, and I was wondering if there's any way to determine the electronic configuration of the excited states. I've been using the pop=npa keyword, but this only details the ground state of the complex. Any help would be greatly appreciated. Thanks in advance, Caroline Norris cn29]*[sussex.ac.uk From owner-chemistry@ccl.net Tue Nov 7 12:44:00 2006 From: "Manish Sud msud~!~sdsc.edu" To: CCL Subject: CCL: Availability of SD file for LIPID MAPS Structure Database Message-Id: <-32954-061107110703-1609-uhQ/2i1PnZfP2RtelKC9Vw-$-server.ccl.net> X-Original-From: "Manish Sud" Date: Tue, 7 Nov 2006 11:07:01 -0500 Sent to CCL by: "Manish Sud" [msud-$-sdsc.edu] On behalf of the LIPID Metabolites And Pathways Strategy (LIPID MAPS) consortium, I would like to announce the availability of SD file for LIPID MAPS Structure Database (LMSD). The LMSD is a growing database containing structures and annotations of biologically relevant lipids. Please visit http://www.lipidmaps.org/data/structure/index.html for further details about the LMSD and to download the SD file. Manish Sud msud[]sdsc.edu From owner-chemistry@ccl.net Tue Nov 7 13:52:01 2006 From: "Sandeep Kumar kumarsan(_)jhu.edu" To: CCL Subject: CCL: MD simulations using MMFF94x and MOE Message-Id: <-32955-061107133645-19111-9/BO6zVaZTSJV6IXPsFC1g(~)server.ccl.net> X-Original-From: "Sandeep Kumar" Date: Tue, 7 Nov 2006 13:36:44 -0500 Sent to CCL by: "Sandeep Kumar" [kumarsan],[jhu.edu] Dear Members: I am trying to do MD calculations on a 28 residue peptide using MMFF94X forcefield as implemented in MOE to assess its conformational flexibility. I was wondering if somebody has experience of using MMFF94x forcefield for peptide simulations and how does it compare with other forcefields, say, AMBER or CHARMM? Another related question whether to do implicit solvation or explicit solvation simulations? I mean which is better and usually what should be the time scales for such simulations? Any advices shall be greatly appreciated. Yours sincerely, Sandeep Kumar ----------------------------------------------------------------------- Dr. Sandeep Kumar, Associate Research Scientist, Johns Hopkins University Department of Biology, 106 Mudd Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA. Phone: 410-516-8433, Email: kumarsan!^!jhu.edu. URL: https://jshare.johnshopkins.edu/skumar23/public_html/ Previous URL: http://www.lecb.ncifcrf.gov/~kumarsan From owner-chemistry@ccl.net Tue Nov 7 16:32:01 2006 From: "shaji chempath shaji.chempath.(~).gmail.com" To: CCL Subject: CCL:G: Question about zeolite adsoption Message-Id: <-32956-061107131314-15136-eL5yND+Ze7YbeLvRdimXhA(~)server.ccl.net> X-Original-From: "shaji chempath" Content-Type: multipart/alternative; boundary="----=_Part_10425_25722339.1162919401550" Date: Tue, 7 Nov 2006 10:10:01 -0700 MIME-Version: 1.0 Sent to CCL by: "shaji chempath" [shaji.chempath],[gmail.com] ------=_Part_10425_25722339.1162919401550 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline You can have a look at the MuSiC code on our website. ( http://zeolites.cqe.northwestern.edu/Music) Its very good for studying adsorption and diffusion in zeolites and other microporous materials. However , MuSiC is an F90 suite of programs ideally suited for running on linux workstations. Also it is purely MM no QM. Shaji On 11/7/06, Jimmy Lawrence jlawrencea/slb.com wrote: > > Sent to CCL by: Jimmy Lawrence [jlawrence^slb.com] > Can anyone share their experiences on calculating gas molecules adsoption > on > zeolites using recent free/ commercial QM/MD softwares ? (such as > Gaussian03, Materials Studio, Spartan, etc) > > I am interested in purchasing software that can give me qualitative > interpretation of gas molecules diffusion inside the zeolite cage, can you > share your experiences/recommendation ? > > Btw, personally QMD program looks very interesting, however I have no > experiences on using it. It would be helpful if any of you can give > advices > about this, since being a Linux beginner, I prefer Windows system. > > Regards, > -------------------------------------- > Jimmy Lawrence > JAPAN > --------------------------------------> > > > ------=_Part_10425_25722339.1162919401550 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline You can have a look at the MuSiC code on our website.  (http://zeolites.cqe.northwestern.edu/Music) Its very good for studying adsorption and diffusion in zeolites and other microporous materials. However , MuSiC is an F90 suite of programs ideally suited for running on linux workstations. Also it is purely MM no QM.
Shaji


On 11/7/06, Jimmy Lawrence jlawrencea/slb.com <owner-chemistry++ccl.net> wrote:
Sent to CCL by: Jimmy Lawrence [jlawrence^slb.com]
Can anyone share their experiences on calculating gas molecules adsoption on
zeolites using recent free/ commercial QM/MD softwares ? (such as
Gaussian03, Materials Studio, Spartan, etc)

I am interested in purchasing software that can give me qualitative
interpretation of gas molecules diffusion inside the zeolite cage, can you
share your experiences/recommendation ?

Btw, personally QMD program looks very interesting, however I have no
experiences on using it. It would be helpful if any of you can give advices
about this, since being a Linux beginner, I prefer Windows system.

Regards,
--------------------------------------
Jimmy Lawrence
JAPAN
--------------------------------------



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------=_Part_10425_25722339.1162919401550-- From owner-chemistry@ccl.net Tue Nov 7 17:07:00 2006 From: "James Robinson James.Robinson#prosonix.co.uk" To: CCL Subject: CCL: [CCL]RE: Excited state electronic configurations Message-Id: <-32957-061107133616-19029-uNy46x+EILo1kNckC1/Z/g+*+server.ccl.net> X-Original-From: "James Robinson" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 7 Nov 2006 18:35:59 -0000 MIME-Version: 1.0 Sent to CCL by: "James Robinson" [James.Robinson]^[prosonix.co.uk] Hi, If memory serves try to include iop(6/7=3) pop=full gfinput and nosymm keyword. Also try to use doublet excited state, and maybe try unrestricted hamiltonian too, so change 0 1 to 0 2. I am not an expert on this, just adding my 2 pence worth. If I am wrong, I would like to be reminded of my own dimness. Dr James Robinson Prosonix, UK. -----Original Message----- > From: owner-chemistry[#]ccl.net [mailto:owner-chemistry[#]ccl.net] Sent: 07 November 2006 17:16 To: James Robinson Subject: CCL: Excited state electronic configurations Sent to CCL by: "Caroline Norris" [cn29::sussex.ac.uk] Dear All, I am in the process of calculating the potential energy curves of the lowest lying excited state of neutral vanadium oxide, and I was wondering if there's any way to determine the electronic configuration of the excited states. I've been using the pop=npa keyword, but this only details the ground state of the complex. Any help would be greatly appreciated. Thanks in advance, Caroline Norris cn29::sussex.ac.ukhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Nov 7 17:42:00 2006 From: "James Robinson James.Robinson%%prosonix.co.uk" To: CCL Subject: CCL: Starter in computational catalysis Message-Id: <-32958-061107132541-17414-sF/Z4oayBIqknzUNeK1vzg- -server.ccl.net> X-Original-From: "James Robinson" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 7 Nov 2006 18:25:12 -0000 MIME-Version: 1.0 Sent to CCL by: "James Robinson" [James.Robinson%prosonix.co.uk] I have only designed a single metallic catalyst by modelling the TS, with only 1 (ONE!) imaginary vibrational frequency. Be careful in your choice of functional, B3LYP does not fit all. Also be careful in selection of basis set, you will need at least 6-311+(2d,p), in my opinion, to have energies that are sufficiently robust to allow to differentiate between pathways. The PBE0 functional will yield nice geometries but some energies are not robust, B3PW91 is another popular choice for metal TS. Couple cluster techniques, such as CCSD or indeed QCISD(T) give lovely energies and structures, but take much longer to calculate. You must not completely ignore relavistic effects when considering heavier metals such as indium etc.. But other know this topic better than I. James Robinson Senior Scientist Prosonix, UK. -----Original Message----- > From: owner-chemistry*ccl.net [mailto:owner-chemistry*ccl.net] Sent: 07 November 2006 02:52 To: James Robinson Subject: CCL: Starter in computational catalysis Sent to CCL by: "Kaci Tizi_Ouzou" [kaci.tiziouzou^^gmail.com] ------=_Part_41969_29885562.1162841287642 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Greetings all, I am trying to start some work on heteregenous catalysis involving polymerisation and I wonder whether anybody can suggest few references describing the process of computing theormo-chemical properties, and reaction dynamics (in the context of catalysis). It appears from my prelimanty readings that DFT is the way to go especially because by catalyst has metallic ions but as a starter I'd like to have the opinion of those who have done such things before. Thanks all, Kaci ------=_Part_41969_29885562.1162841287642 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Greetings all,
 
I am trying to start some work on heteregenous catalysis involving polymerisation and I wonder whether anybody can suggest few references describing the process of computing theormo-chemical properties, and reaction dynamics (in the context of catalysis).
 
It appears from my prelimanty readings that DFT is the way to go especially because by catalyst has metallic ions but as a starter I'd like to have the opinion of those who have done such things before.
 
 
 
 
Thanks all,
 
 
Kaci

------=_Part_41969_29885562.1162841287642--http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt