From owner-chemistry@ccl.net Wed Jan 7 05:19:00 2009 From: "Andreas Bick andreas.bick++scienomics.com" To: CCL Subject: CCL: molecular mechanics and dynamics for metal-organic and organic-organic Message-Id: <-38398-090107051020-1676-YsFspdSk0tyOl+WKMfqfyA(0)server.ccl.net> X-Original-From: Andreas Bick Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Wed, 07 Jan 2009 10:28:06 +0100 MIME-Version: 1.0 Sent to CCL by: Andreas Bick [andreas.bick(-)scienomics.com] Hi Egbert, you can also try LAMMPS( http://lammps.sandia.gov/) or NAMD(http://www.ks.uiuc.edu/Research/namd/). Andreas > Sent to CCL by: "Jim Kress" [ccl_nospam _ kressworks.com] > Try gromacs > > http://www.gromacs.org/ > > There are other packages but this one meets your "free" requirement :>} > > Jim > > >> -----Original Message-----http://www.ks.uiuc.edu/Research/namd/ >> From: owner-chemistry+ccl_nospam==kressworks.com],[ccl.net >> [mailto:owner-chemistry+ccl_nospam==kressworks.com],[ccl.net] >> On Behalf Of Egbert Zojer egbert.zojer.:.tugraz.at >> Sent: Monday, January 05, 2009 11:11 AM >> To: Kress, Jim >> Subject: CCL: molecular mechanics and dynamics for >> metal-organic and organic-organic >> >> >> Sent to CCL by: "Egbert Zojer" [egbert.zojer]_[tugraz.at] Dear all, >> >> For the past few years, we have used density functional >> theory to describe the properties of metal organic systems. >> These include self-assembled monolayers on noble metals, or >> strong organic acceptors and donors (experiencing significant >> charge transfer when bonded to the metal surface) >> >> As a complementary approach (bearing in mind all the >> limitations of DFT, like the inability to describe dispersion >> forces, which to our experience only partly overcome by >> non-local functionals + to be able to describe much larger >> and more complex systems), I would like to try out approaches >> based on classical force fields (in particular MD). >> Unfortunately, I know not much about such force fields apart >> from their "general properties". >> >> Therefore, I would be grateful about information on force >> fields (+ suitable computar codes - if possible available >> free of charge) with a proven track-record in >> * describing the interaction between conjugated organic molecules, >> * possibly also reasonably well parametrized to describe >> interactions between organic molecules and noble (or not so >> noble) metals in the absence of metal-organic charge transfer. >> * codes that would also allow to include charged species (if >> necessary to be calculated on the DFT level. >> * info on shortcomings to be expected when applying such an >> approach that a person with only a rudimentary understanding >> of force fields might overlook. >> >> Thanks a lot in advance, >> >> Egbert >> >> >> >> -= This is automatically added to each message by the mailing >> script =- To recover the email address of the author of the >> message, please change the strange characters on the top line >> to the ],[ sign. You can also look up the X-Original-From: line >> in the mail header.> Conferences: >> http://server.ccl.net/chemistry/announcements/conferences/ >> >> Search Messages: http://www.ccl.net/htdig (login: ccl, >> Password: search)> > > > -- Dr. Andreas Bick Scienomics SARL Sales and Marketing mobile: +491621309945 From owner-chemistry@ccl.net Wed Jan 7 18:23:00 2009 From: "Leyla Ramin lram5228=-=usyd.edu.au" To: CCL Subject: CCL: MD code Message-Id: <-38399-090107182107-9553-qijkChqsSs1VzCRETZ2PMw^^server.ccl.net> X-Original-From: "Leyla Ramin" Date: Wed, 7 Jan 2009 18:21:02 -0500 Sent to CCL by: "Leyla Ramin" [lram5228%a%usyd.edu.au] Hi, I am wondering if anybody has the available fortran code for MD of Lennard jones molecules including Link cell method and Neighbour list together? I already tried to use the code in CCL website but when I tried to put the neighbour list and link cell together, The result that I get is not so accurate. Best Regards Leila From owner-chemistry@ccl.net Wed Jan 7 20:32:01 2009 From: "Joy P. Ku joyku\a/stanford.edu" To: CCL Subject: CCL: OpenMM Workshop: Speeding up molecular dynamics on GPUs Message-Id: <-38400-090107172403-4848-TSV2hu6xlMayg7/XHIT1vQ|,|server.ccl.net> X-Original-From: "Joy P. Ku" Date: Wed, 7 Jan 2009 17:24:00 -0500 Sent to CCL by: "Joy P. Ku" [joyku{=}stanford.edu] Want to learn how to quickly set up and run molecular dynamics (MD) simulations? Or are you a veteran to MD who wants to know how to obtain 100X speedups of MD code on GPUs?* Whatever your MD background, the free upcoming two-day OpenMM workshop promises to be an exciting, knowledge-filled opportunity, featuring experts from both molecular dynamics and the GPU industry. Day 1 of the workshop is geared towards MD developers and will discuss how MD code can be sped up on GPUs and in particular, with the new OpenMM 1.0 library. OpenMM is a freely downloadable, high performance, extensible library that allows MD simulations to run on high performance computer architectures, such as graphics processing units (GPUs). Day 2 of the workshop is for researchers interested in using MD in their research, including novices to MD. You will learn the theory behind MD and use the new OpenMM Zephyr application, which makes it easy to run and visualize MD simulations. The workshop will be held on February 12-13, 2009 at Stanford University. Registration is free but required and spaces are limited. You can sign up for one or both days. For more details, visit http://simbios.stanford.edu/EventsOfInterest/OpenMMWorkshop.htm. We hope to see you there! Joy P. Ku Director of Dissemination Simbios, Stanford University Email: joyku/a\stanford.edu --------------------------------------------------------------------- OpenMM and OpenMM Zephyr are supported by Simbios, an NIH National Center for Physics-Based Simulation of Biological Structures, as part of its protein folding research efforts. To learn more about Simbios and its research and software tools, visit http://simbios.stanford.edu. *OpenMM accelerated code running on Nvidia GeForce GTX 280 GPU vs. conventional code with Amber9 running on Intel Xenon 2.66 GHz CPU. MS Friedrichsm, et al., "Accelerating Molecular Dynamic Simulation on Graphics Processing Units," J. Comp. Chem., in press.