From owner-chemistry@ccl.net Fri Nov 14 09:33:01 2008 From: "Andrew R Turner andrew.turner(~)ed.ac.uk" To: CCL Subject: CCL: MPI Message-Id: <-38109-081114050537-29362-Td697rzBLoPFb8NWq8Kibg{:}server.ccl.net> X-Original-From: Andrew R Turner Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Fri, 14 Nov 2008 09:30:04 +0000 MIME-Version: 1.0 Sent to CCL by: Andrew R Turner [andrew.turner|a|ed.ac.uk] Hi John, Could you provide the detials of your hardware, OS and compilers? Specifically: * Processor type (& number) * Interconnects * OS (+ kernel version) * Compiler * Issues you are having; error messages from compile, etc. Then we might be able to provide some more help. Cheers Andy ======================================== Dr Andrew R. Turner e: andrew.turner,,ed.ac.uk t: +44 (0)131 651 3578 p: Edinburgh Parallel Computing Centre University of Edinburgh EH9 3JZ ======================================== -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From owner-chemistry@ccl.net Fri Nov 14 10:40:01 2008 From: "Lucius E Johnson lejohn07]~[louisville.edu" To: CCL Subject: CCL:G: NMR shielding Effects Message-Id: <-38110-081114103752-20936-mRUrwddZPKD1zs/G7shebA{=}server.ccl.net> X-Original-From: "Lucius E Johnson" Date: Fri, 14 Nov 2008 10:37:47 -0500 Sent to CCL by: "Lucius E Johnson" [lejohn07-#-louisville.edu] Hi Mr. Shabbir, First, I want to make sure I understand your change in shifts, because the terminology seems backwards. A downfield shift will cause a higher chemical SHIFT value due to a lower chemical SHIELDING value. The chemical shift is calculated by subtracting the isotropic shielding value from the calculated reference value (TMS for C and H). For instance, a proton shift at 10ppm is downfield from one at 2ppm. The proton at 10ppm is more deshielded and has a lower isotropic shielding value. The calculated shielding value (if using GIAO) comes from two components- the diamagnetic component, related to the electron density in a magnetic field, and the paramagnetic, related to the movement of electrons from occupied to vacant orbitals in the presence of the mag. field. The paramagnetic term is dependent upon the energy differences between occupied and vacant orbitals, their populations, and the orbital angular momentum operator that causes their overlap. (Ramsey formalism) Changes in isotropic shielding values are dominated by the paramagnetic term, which is much more sensitive to changes in geometry and electron density distribution. So I guess before answering we need to clarify a couple things -Do the two atoms and their Hydrogens have higher chemical SHIFT values, or higher chemical SHIELDING values? -How do the HOMO and LUMO (and other energetically close) orbitals change upon forming the complex? This will provide a more complete link to the changes in shielding values. In general, changes in shielding and shifts are more dependent on how the electron density is distributed (paramagnetic term) than just in the total density surrounding a nucleus. I don't think you can say that just because the HOMO isn't around the hydrogens, they are necessarily more deshielded- it is really going to depend on the currents. You can get the separation of the diamagnetic and paramagnetic terms of the isotropic shielding tensor- in Gaussian, use "nmr iop33(10=1) in the route line. You can also create cube files to visualize how the electronic currents in a magnetic field cause the shielding or deshielding of each nucleus. Let me know if you want help with that- it's a little time consuming. Here's a helpful reference for calculated NMR shielding values- see especially section 5. Wiberg et al, J. Phys Chem A., 1999, 103, pp21-27 Hope this helps a little! Let me know if you have more questions/info. Lucius Johnson lejohn07*louisville.edu From owner-chemistry@ccl.net Fri Nov 14 11:25:00 2008 From: "John McKelvey jmmckel=gmail.com" To: CCL Subject: CCL: MPI Message-Id: <-38111-081114112305-11252-Tixf4Kam84fPqpXBXzr6kg ~~ server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_9932_24822095.1226679771472" Date: Fri, 14 Nov 2008 11:22:51 -0500 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel-#-gmail.com] ------=_Part_9932_24822095.1226679771472 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Andy, Dual AMD64 Opteron 270 (dual-core) Run on a single 4-processor box in SMP OS: RHEL4, Kernel:2.6.9-42 (64bit) Default + Intel 10 compiler (don't know what was used for ORCA) At beginning of SCF: fails on opening guess file (test.gbw, which is there and seems of appropriate size) Thanks! John On Fri, Nov 14, 2008 at 4:30 AM, Andrew R Turner andrew.turner(~)ed.ac.uk < owner-chemistry^ccl.net> wrote: > > Sent to CCL by: Andrew R Turner [andrew.turner|a|ed.ac.uk] > > Hi John, > > Could you provide the detials of your hardware, OS and compilers? > Specifically: > > * Processor type (& number) > * Interconnects > * OS (+ kernel version) > * Compiler > * Issues you are having; error messages from compile, etc. > > Then we might be able to provide some more help. > > Cheers > > Andy > > ======================================== > Dr Andrew R. Turner > e: andrew.turner#ed.ac.uk > t: +44 (0)131 651 3578 > p: Edinburgh Parallel Computing Centre > University of Edinburgh > EH9 3JZ > ======================================== > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336.http://www.ccl.net/chemistry/sub_unsub.shtml> > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > ------=_Part_9932_24822095.1226679771472 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Andy,

Dual AMD64 Opteron 270 (dual-core)
Run on a single 4-processor box in SMP
OS: RHEL4, Kernel:2.6.9-42 (64bit)
Default + Intel 10 compiler  (don't know what was used for ORCA)
At beginning of SCF: fails on opening guess file (test.gbw, which is there and seems of appropriate size)


Thanks!

John



On Fri, Nov 14, 2008 at 4:30 AM, Andrew R Turner andrew.turner(~)ed.ac.uk <owner-chemistry^ccl.net> wrote:

Sent to CCL by: Andrew R Turner [andrew.turner|a|ed.ac.uk]

Hi John,

Could you provide the detials of your hardware, OS and compilers? Specifically:

* Processor type (& number)
* Interconnects
* OS (+ kernel version)
* Compiler
* Issues you are having; error messages from compile, etc.

Then we might be able to provide some more help.

Cheers

Andy

========================================
    Dr Andrew R. Turner
 e: andrew.turner#ed.ac.uk
 t: +44 (0)131 651 3578
 p: Edinburgh Parallel Computing Centre
    University of Edinburgh
    EH9 3JZ
========================================

--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



E-mail to subscribers: CHEMISTRY^ccl.net or use:
    http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST^ccl.net or use
    http://www.ccl.net/cgi-bin/ccl/send_ccl_message
http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobsConferences: http://server.ccl.net/chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/htdig  (login: ccl, Password: search)
    http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/



------=_Part_9932_24822095.1226679771472-- From owner-chemistry@ccl.net Fri Nov 14 17:14:00 2008 From: "Jonathan Moore jmoore2]=[dow.com" To: CCL Subject: CCL: FOMMS 2009 Message-Id: <-38112-081114171218-17434-3RpsV2yi+fftzOctASjPbg]*[server.ccl.net> X-Original-From: "Jonathan Moore" Date: Fri, 14 Nov 2008 17:12:14 -0500 Sent to CCL by: "Jonathan Moore" [jmoore2{=}dow.com] The first circular for FOMMS 2009 is reproduced in this email below. Please forward to anyone who would be interested. Fourth International Conference Foundations of Molecular Modeling and Simulation FOMMS 2009 Foundations for Innovation Semiahmoo Resort, Blaine, WA, USA July 12 -16, 2009 http://fomms.org Presented by: CACHE Corporation and the Computational Molecular Science & Engineering Forum of the American Institute of Chemical Engineers FOMMS 2009 is the 4th international conference showcasing applications and theory of computational quantum chemistry, molecular science, and engineering simulation. It is motivated by the continual need for precise prediction and control of materials properties and the fundamental, molecular-level understanding of chemical processes that allow the efficient creation of new products to meet specific market demands. Theoretical and algorithmic advances and modern computing technology allow companies to capture value and truly sustainable, far-reaching competitive advantage. The future for these methods is bright as they continue to prove their value to the chemical and chemical-related industries. The conference will explore these issues in the same format as the three previous highly successful FOMMS meetings held in 2000, 2003, and 2006. Whats new this time? - Focus on foundations and applications - Afternoon and evening workshop on special topics like open source code development and interoperability, and new multicore processors and gpus - Founder's Medal & lecture, followed by banquet - Ending on Thursday night after banquet FOMMS 2009 is a scientific modeling meeting balanced between molecular simulation and computational chemistry. All talks are invited and represent the state-of-the-art in the particular special topic areas. Two poster sessions will provide opportunities for all attendees to present their work. Also, one afternoon will be devoted to a workshop on the use of multicore and GPUs, and an evening workshop on open source code development will also be featured. In addition, the schedule provides large blocks of time for informal discussions, relaxation, or leisure, as well as several receptions to facilitate interaction between conference participants. Each presentation will be rigorously reviewed and edited. Invited Speakers* New perspectives in molecular simulation: - Daan Frenkel (Cambridge) - Berend Smit (UC Berkeley) Proteins and biological systems: - David Baker (UW) - Charlie Brooks (UM) Linking process scale simulation and molecular modeling: - Linda Broadbelt (NWU) - Dion Vlachos (U Delaware) Rare events: acceleration algorithms and transition path sampling: - Baron Peters (UCSB) - Giovanni Ciccotti (La Sapienza, Rome) - Phil Geissler (UC Berkeley) Soft materials and complex fluids: - Ilja Siepmann (U Minn) - Clare McCabe (Vanderbilt) - Lev Gelb (Wash U) Simulation-based engineering & science - Novel materials and industrial applications: - Caroline Mellot (UCL, UK) - Shinichiro Nakamura (Mitsubishi, Japan) - Herve' Toulhoat (IFP, France) Petascale computing and emerging architectures for modeling and simulation: - David Shaw (D.E. Shaw Research & Columbia) - Klaus Schulten (UIUC) - George Karniadakis (Brown U.) * all confirmed Call for Participation FOMMS is the premier conference on molecular modeling and simulation. Through a combination of outstanding keynote and invited talks on cutting edge research, to tutorials and workshops on selected topics, FOMMS caters to all levels of interest, from the expert in molecular modeling and simulation to those interested in learning more about this exciting field. FOMMS 2009 will bring together in a single forum the best molecular modeling researchers, academic and industrial users, and commercial vendors. To subscribe to the FOMMS information mailing list, visit http://www.freelists.org/list/fomms or send an email to fomms-request]*[freelists.org with subscribe in the subject field. For more info or to contact the organizers, http://fomms.org Important Dates - Submission of poster abstracts: February 13, 2009 - Notification of poster acceptance: March 27, 2009 - Invited talk and poster manuscripts due: (for inclusion in conference cd) June 5, 2009 - Early registration deadline: June 5, 2009 - Cut-off date for hotel reservations: June 12, 2009 - Conference: July 12-16, 2009 Venue The Semiahmoo Resort is a seaside hotel featuring a luxurious spa and two of Washingtons top public courses; Loomis Trail Golf Club and Semiahmoo Golf & Country Club. Nestled on the northern Puget Sound shoreline in Blaine, Washington, and overlooking Semiahmoo Bay and Drayton Harbor, Semiahmoo offers a multitude of resort activities in an exceptional setting. http://www.semiahmoo.com/ Conference Organizing Committee Chair: Sharon Glotzer (U Michigan) Co-Chairs Alain Fuchs (ENSPC) Susumu Okazaki (IMS) Jonathan Moore (Dow Chemical) Senior Advisors Peter T. Cummings (Vanderbilt/ORNL) Phil Westmoreland (UMass/NSF) Joe Golab (INEOS) Programming committee Claire Adjiman (Imperial College) Jerry Bernholc (NCSU) Anne M. Chaka (NIST) Pablo Debenedetti (Princeton) Kerwin Dobbs (Dupont) Thom Dunning (NCSA) Glenn Fredrickson (UCSB) Shekhar Garde (RPI) Peter A. Gordon (ExxonMobil) Carol K. Hall (NCSU) Mark A. Horsch (Intel) Shiaki Hyodo (Toyota Central R&D) David A. Kofke (SUNY-Buffalo) Shaoyi Jiang (UW) Matthew Neurock (UVa) Jeffrey A. Nichols (ORNL) John P. O'Connell (UVa) Mark A. Ratner (NWU) Richard Ross (3M) Philippe Ungerer (IFP) Sponsorship Opportunities Vendors and organizations are invited to participate as sponsors of FOMMS 2009. To indicate your interest, contact admin]*[fomms.org Jonathan Moore jmoore2]*[dow.com