From owner-chemistry@ccl.net Tue Apr 17 02:07:01 2007 From: "Niklas Loges niklas.loges::web.de" To: CCL Subject: CCL: Accelrys Materials Studio, Amorphous Cell Message-Id: <-34064-070417020514-27283-OLfRVEHICHvqUaqqvdvRCA-#-server.ccl.net> X-Original-From: "Niklas Loges" Date: Tue, 17 Apr 2007 02:05:10 -0400 Sent to CCL by: "Niklas Loges" [niklas.loges|web.de] Hi everyone, I'm calculating interaction energies between crystal surfaces, which I obtain by cleaving the original crystal structures, and amoprhous layers of small molecules. The layers were produced with the amorphous cell-tool within Accelrys Materials Studio. The problem is that some of my crystal surfaces have angles of 60 or 120 and my question is, if there is a possibility to produce amorphous cells with these angles. Thanks a lot! Niklas Loges -- Dipl. Chem. Niklas Loges Johannes Gutenberg-Universitt Institut fr Anorganische und Analytische Chemie Arbeitskreis Prof. W. Tremel Forschung Sd, Raum 03-114 Duesbergweg 10-14 55099 Mainz Tel.: (06131) 39-23920 From owner-chemistry@ccl.net Tue Apr 17 04:27:01 2007 From: "David Cornil cornildavid%yahoo.fr" To: CCL Subject: CCL: effective_potential Message-Id: <-34065-070417042328-27966-Pq5mXeo240Axvs+i3eHBCg%server.ccl.net> X-Original-From: "David Cornil" Date: Tue, 17 Apr 2007 04:23:24 -0400 Sent to CCL by: "David Cornil" [cornildavid**yahoo.fr] Dear CCl's users, Can anyone suggest me references about use or computation of effective potentials bewtween an atom and a periodic surface ? O (atom) | | (z = normal distance to surface) | X X X X X X X (surface) < x > Do you know some works when the interaction potential is simulated and how we can deal with the sum of 1/r^n interaction when r is the distance between O (isolated atom) and each surface atom ? Thank you in advance David From owner-chemistry@ccl.net Tue Apr 17 13:25:05 2007 From: "Thanh N. Truong truong]=[chemistry.chem.utah.edu" To: CCL Subject: CCL: CSE-Online -- Computational Chemistry Environment Message-Id: <-34066-070417125210-5456-hnR6G9kgjLoPyytDwVW8Og||server.ccl.net> X-Original-From: "Thanh N. Truong" Content-Type: multipart/alternative; boundary="----=_NextPart_000_001D_01C780D7.06103D40" Date: Tue, 17 Apr 2007 09:59:01 -0600 MIME-Version: 1.0 Sent to CCL by: "Thanh N. Truong" [truong-.-chemistry.chem.utah.edu] This is a multi-part message in MIME format. ------=_NextPart_000_001D_01C780D7.06103D40 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit Teaching and learning computational chemistry have never been simpler! CSE-Online provides a user-friendly and intuitive cyber-environment that enables efficient and secure access to remote tools, data, and computing resources. With CSE-Online, you can teach or learn computational chemistry without worrying about: 1. The need for a computing lab. Students can use their laptops in a standard classroom--or anywhere else that has an Internet connection. 2. The need to purchase, install and maintain modeling tools. With CSE-Online, the modeling tools are available from the TeraGrid. 3. The need for local high-performance computers. The TeraGrid awarded CSE-Online 200,000 CPU hours on supercomputers at the National Center for Supercomputing Applications. Any CSE-Online registered users can use these resources for learning or teaching between April 2007 and March 2008. No user account on the TeraGrid is required. My undergraduate physical chemistry students describe using CSE-Online as "having fun playing while learning." See CSE-Online in action Suenaga, Isobe, Nakamura and co-workers recently showed that trapping organic molecules in a carbon single-wall nanotube can significantly slow down their motion, making it possible to observe the molecules with transmission electron microscopy. Their results were reported in Science (Feb. 22, 2007 Issue: DOI: 10.1126/science.113869), http://www.ccl.net/images/stuffed-nanotube.jpg With the MolDesign tool in CSE-Online, a student from any location connected to the Internet can model and obtain insight into the system in less than five minutes: two minutes for building the model and submitting the job, one minute waiting in the computing queue, one minute for the calculation, and one minute for gaining insight into the reasons the motion of the organic molecule is slowed in the nanotube. Watch the five-minute movie that captured the real-time modeling process: http://www.cse-online.net/movies/10-MolDesign/flash2.2/Moving-in-SWNT-Test_1024x768.html Read GridToday's article about CSE-Online: http://www.gridtoday.com/grid/1338891.html Can you perform such a modeling yourself? Yes, and you can do much more. To get started: 1.Go to http://CSE-Online.net to register for a free user account. 2.Run the Installer (information is available on the CSE-Online homepage). 3. Run the connection test (from the CSE-Online homepage) 4.Open the MolDesign tool. Under the Help menu, choose the 'Tour Manager' and go through the short self-guided lessons. There are a number of practical exercises available in the QChem Exercises link at the CSE-Online web site that you can use for your classes or for practice. ----------------------------------------------------------------------- Thanh N. Truong, Professor Henry Eyring Center for Theoretical Chemistry Department of Chemistry University of Utah 315 South 1400 East, rm 2020 Salt Lake City, UT 84112 Phone: (801) 581-4301 Fax: (801) 581-4353 Web: http://truong.hec.utah.edu Email: Truong*_*chemistry.utah.edu ------=_NextPart_000_001D_01C780D7.06103D40 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable

Teaching and learning = computational chemistry have never been simpler!

 

CSE-Online provides a = user-friendly and intuitive cyber-environment that enables efficient and secure access = to remote tools, data, and computing resources. With CSE-Online, you can = teach or learn computational chemistry without worrying = about:

 

1. The need for a computing = lab. Students can use their laptops in

   a standard classroom--or anywhere else that has an Internet = connection.

 

2. The need to purchase, = install and maintain modeling tools. With

   CSE-Online, = the modeling tools are available from the = TeraGrid.

 

3. The need for local high-performance computers. The TeraGrid = awarded

   CSE-Online = 200,000 CPU hours on supercomputers at the National Center

   for = Supercomputing Applications. Any CSE-Online registered users = can

   use these = resources for learning or teaching between April 2007 and

   March 2008. No = user account on the TeraGrid is required.

 

My undergraduate physical = chemistry students describe using CSE-Online as "having fun playing while learning."

 

See CSE-Online in = action

 

Suenaga, Isobe, Nakamura = and co-workers recently showed that trapping organic molecules in a carbon single-wall nanotube can significantly slow down their motion, making it possible to observe the molecules with transmission electron microscopy. = Their results were reported in Science (Feb. 22, 2007 Issue: DOI: 10.1126/science.113869), http://www.ccl.ne= t/images/stuffed-nanotube.jpg

 

With the MolDesign tool in CSE-Online, a student from any location connected to the Internet can = model and obtain insight into the system in less than five minutes: two minutes = for building the model and submitting the job, one minute waiting in the = computing queue, one minute for the calculation, and one minute for gaining = insight into the reasons the motion of the organic molecule is slowed in the = nanotube.

 

Watch the five-minute movie = that captured the real-time modeling process:

http://www.cse-online.net/movies/10-MolDesign/fl= ash2.2/Moving-in-SWNT-Test_1024x768.html

=

 

Read GridToday's article = about CSE-Online:  http://www.gridtoday.= com/grid/1338891.html

 

Can you perform such a = modeling yourself? Yes, and you can do much more.

To get = started:

 

1.Go to http://CSE-Online.net to register = for a free user account.

 

2.Run the Installer = (information is available on the CSE-Online homepage).

 

3. Run the connection test = (from the CSE-Online homepage)

 

4.Open the MolDesign tool. = Under the Help menu, choose the 'Tour Manager'

  and go through the = short self-guided lessons.

 

There are a number of = practical exercises available in the QChem Exercises link at the CSE-Online web = site that you can use for your classes or for = practice.

 

 

------------------------------------------------------= -----------------

Thanh N. Truong, = Professor

 

Henry Eyring Center for Theoretical Chemistry

Department of Chemistry

University of Utah

=

315 South 1400 East, rm = 2020

Salt = Lake City, UT 84112

 

Phone: (801) 581-4301

Fax:     (801) = 581-4353

Web:    http://truong.hec.utah.edu=

Email:   Truong*_*chemistry.utah.edu

 

 

------=_NextPart_000_001D_01C780D7.06103D40-- From owner-chemistry@ccl.net Tue Apr 17 15:29:00 2007 From: "Boyd, D. boyd^-^chem.iupui.edu" To: CCL Subject: CCL: Gordon Conference on Computational Chemistry Message-Id: <-34067-070417151021-12263-SyWYTT1KPiFQ4gR8sXBuvQ^server.ccl.net> X-Original-From: "Boyd, D." Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Tue, 17 Apr 2007 15:09:52 -0400 MIME-Version: 1.0 Sent to CCL by: "Boyd, D." [boyd~!~chem.iupui.edu] Colleagues, Photos and information about last fall's Gordon Research Conference on Computational Chemistry are posted at http://chem.iupui.edu/rcc/grccc.html. Also, the website has information about the next conference. Thanks, Donald B. Boyd Department of Chemistry and Chemical Biology Indiana University-Purdue University at Indianapolis From owner-chemistry@ccl.net Tue Apr 17 17:49:01 2007 From: "Andrew Orry andy-x-molsoft.com" To: CCL Subject: CCL: Workshop: Modern Drug Target Crystallography and Structure Based Drug Discovery Message-Id: <-34068-070417174129-17510-KIZgy792kc6ArT6qtAI3HQ^server.ccl.net> X-Original-From: Andrew Orry Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Tue, 17 Apr 2007 13:40:17 -0700 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [andy^molsoft.com] A two day workshop on the cutting-edge developments in crystallography and structure based drug design will be held on June 28th-29th, 2007 in La Jolla California. Information regarding registration and course content can be found here: http://www.ruppweb.org/workshops/Molsoft_workshop_2007.htm The workshop entitled "Modern Drug Target Crystallography and Structure Based Drug Design" is suitable for executives, scientists, and technicians in the field of biological sciences, chemistry and drug discovery, who wish to expand their knowledge in the rapidly advancing field of high throughput drug target crystallography and structure guided drug discovery. The course will be conducted by: Dr. Bernhard Rupp (Founder qed life science discoveries, inc) and Prof. Ruben Abagyan (Professor of Molecular Biology at The Scripps Research Institute and Founder of Molsoft LLC). The workshop includes protein crystallization demonstrations, actual structure determination using multiple anomalous dispersion methods and molecular replacement, model building and refinement, structure validation, analysis and interpretation, followed by in-silico ligand docking and virtual ligand screening. For more information please visit: http://www.ruppweb.org/workshops/Molsoft_workshop_2007.htm E mail: andy%x%molsoft.com or call (858 625 2000 x108). Places are limited (12 participants) so early enrollment is encouraged.