From owner-chemistry@ccl.net Thu Apr 24 05:47:00 2014 From: "Hyungjun Kim hyungjun96::kaist.ac.kr" To: CCL Subject: CCL: Force constant in Gaussian09 Message-Id: <-49959-140424054349-25944-fbiJ8S24KCoLl+21ZxNysg!A!server.ccl.net> X-Original-From: "Hyungjun Kim" Date: Thu, 24 Apr 2014 05:43:48 -0400 Sent to CCL by: "Hyungjun Kim" [hyungjun96 ~ kaist.ac.kr] Dear CCL subscribers, I'm trying to obtain the force constants (k) of large metal complexes. 'OPT FREQ=internal' calculations is performed. I find that some bonds are changed together and I cannot get the separate k value for each bond. How can I separate this value? Is it related to the diagonalization of a hessian matrix which reported at CCL some days ago? If then, are there any tools that are capable of doing this work? Thank you for any comments in advance. From owner-chemistry@ccl.net Thu Apr 24 08:23:00 2014 From: "Jasleen Kaur jasleen.chem_+_gmail.com" To: CCL Subject: CCL: problem involving endothermic adsorption Message-Id: <-49960-140424030804-28194-c6EHEPHW19INTVPoDCdd4g]^[server.ccl.net> X-Original-From: "Jasleen Kaur" Date: Thu, 24 Apr 2014 03:08:03 -0400 Sent to CCL by: "Jasleen Kaur" [jasleen.chem^^gmail.com] My work involves the DFT studies on the interaction of the organic molecule over the nanotubes. My problem is can endothermic adsorption of a molecule over the nanotube surface cause significant change in structural and electronic properties?, as in my case. What is the significance of such an unstable adsorption? Jasleen Kaur jasleen.chem _ gmail.com Panjab University Chandigarh, India From owner-chemistry@ccl.net Thu Apr 24 15:48:00 2014 From: "Andreas Goetz agoetz]*[sdsc.edu" To: CCL Subject: CCL: AMBER Molecular Dynamics Workshop Barcelona Jun 2-6. Pre-Registration Message-Id: <-49961-140424144154-32257-kByFHehVPA68v9MnNtWxIg_+_server.ccl.net> X-Original-From: "Andreas Goetz" Date: Thu, 24 Apr 2014 14:41:52 -0400 Sent to CCL by: "Andreas Goetz" [agoetz..sdsc.edu] Dear all, This is a reminder that pre-registration for the AMBER Molecular Dynamics Workshop to be held in Barcelona June 2nd to 6th 2014 closes on Apr 28th. http://mmb.pcb.ub.es/www/amber2014 Please forward this announcement to any of your colleagues who may be interested. Thank you. ----------------- We are glad to announce the Amber Workshop 2014 that will be held in Barcelona from the 2nd to 6th June at the Vertex Building (UPC Campus). The course will be taught by Ross C. Walker and Adrian E. Roitberg and will be hosted by the IRB Barcelona and the Barcelona supercomputing Center. More info: http://mmb.pcb.ub.es/www/amber2014 Please feel free to forward this announcement to all your contacts. With the best regards, The Organizing Team * Program The duration of the meeting is 5 days, from 2nd of June to 6th. Typically there will be lectures 3 hours per day, and hands-on tutorials, about 5 hours per day. The content of the Workshop will include: * Molecular Dynamics with Amber * Using VMD to visualize AMBER * Dealing with non-standard residues * Building protein-ligand complexes * Statistical Mechanics for Free Energy Calculations * MM/PBSA calculations * Calculating relative binding free energies for protein/carbohydrate complexes * Enhanced sampling techniques * Maximizing Performance (Parallel Execution and NVIDIA GPU Acceleration) * Umbrella sampling simulations * Analyzing Simulations * Introduction to QM/MM Calculations * Lipid Simulations with AMBER The target audience is graduate students and postdocs as well as a few faculty interested in learning about Molecular Dynamics techniques. The course is designed to introduce Molecular Dynamics techniques from an introductory perspective but will progress quickly. Some experience with the Linux operating system is essential but experience with AMBER or other molecular dynamics packages is not required. * Registration The number is limited to 40. Given the limited number of seats you will be requested to fill a pre-registration form. Fill the pre-registration form at: http://mmb.pcb.ub.es/www/amber2014 Important: Pre-registration deadline is 28 of April. Organizers will review applications and invite those selected to register by May 8th. From 8th of May, if there are seats available, the organizers will accept further applications. Registration fees are 190 euros. Attendees are expected to bring their own laptop. The organization will provide a pendrive with all necessary software and training material. Lunch and coffee breaks are included.