From owner-chemistry@ccl.net Fri Apr 22 02:49:00 2011 From: "Joy Ku joyku]![stanford.edu" To: CCL Subject: CCL: Molecular Dynamics Workshop Series - Develop and Analyze Simulations Message-Id: <-44455-110422024604-17226-MmidQXK+hcnisbdZze8wDg ~~ server.ccl.net> X-Original-From: "Joy Ku" Date: Fri, 22 Apr 2011 02:46:02 -0400 Sent to CCL by: "Joy Ku" [joyku=-=stanford.edu] Simbios is excited to announce its upcoming Molecular Dynamics (MD) Workshop Series, highlighting new capabilities within the recently released OpenMM 3.0, including its Python API and integration of the AMOEBA polarizable force field with OpenMM. OpenMM is a freely downloadable library that enables MD simulations to run on high performance computer architectures. It has demonstrated speed ups for both implicit solvent[1] and explicit solvent simulations[2] on GPUs. WHERE: Stanford University WHEN: May 23-24, 2011 (sign up for one or two days) DAY 1: DEVELOPING MOLECULAR DYNAMICS ON GPUS WITH OPENMM For those interested in running MD simulations on graphics processing units (GPUs) and/or developing new MD algorithms that can automatically be implemented and accelerated on GPUs. Some programming background is required. DAY 2: INTRODUCTION TO MOLECULAR DYNAMICS AND TRAJECTORY ANALYSIS WITH MARKOV STATE MODELS For researchers (including novices to MD) interested in using MD and/or analyzing MD results in their research. Deepen your knowledge about MD simulations and gain hands-on experience with using the MSMBuilder software[3] to automatically construct Markov State Models for trajectory analysis. REGISTRATION: Registration is free but required and spaces are limited. To register or for more information, visit http://simbios.stanford.edu/MDWorkshops.htm. ________________________________________ OpenMM and MSMBuilder are supported by Simbios, an NIH National Center for Physics-Based Simulation of Biological Structures. To learn more about Simbios and its research and software tools, visit http://simbios.stanford.edu. [1] OpenMM accelerated code running on NVIDIA GeForce GTX 280 GPU vs. conventional code with Amber9 running on Intel Xenon 2.66 GHz CPU. MS Friedrichs, et al., "Accelerating Molecular Dynamic Simulation on Graphics Processing Units," J. Comp. Chem., 2009, 30(6):864-872. [2]Eastman, P. and Pande, V.S. (2009). Efficient Nonbonded Interactions for Molecular Dynamics on a Graphics Processing Unit. Journal of Computational Chemistry. [3] GR Bowman, X Huang, and VS Pande, "Using generalized ensemble simulations and Markov state models to identify conformational states," Methods, 49(2):197-201. From owner-chemistry@ccl.net Fri Apr 22 17:57:01 2011 From: "Roanld L Cook cookrl{}tda.com" To: CCL Subject: CCL:G: Proxy for aluminum oxide surface Message-Id: <-44456-110422173940-16199-duMIk8V+4xYqEwBYy4cXyA]=[server.ccl.net> X-Original-From: "Roanld L Cook" Date: Fri, 22 Apr 2011 17:39:38 -0400 Sent to CCL by: "Roanld L Cook" [cookrl_+_tda.com] Hi CCLers I have been studying the interactions between organic bases and Al(OH)3. I would like to move onto Al(OAl(OH)2)3 and larger surface segments. Furthermore, I would like the bond lengths and bond angles to be those found in the aluminum surface oxide boehmite (AlOOH). For the Al(OH)3 sudies I am using Gaussian 09 (which may be the wrong tool for the next series of calculations)to calculate the electron densities and then use the fch file as input into AIMALL to carry out atom in molecules electron density topology calculations. My question is (and I have searched the Gaussian manual, the literature and the CCL archives)...is there any way to specify that the Al(OAl(OH)2)3 proxy for the aluminum oxide surface not be (relaxed, energy minimized)but only carry out the energy minimization for the organic and the interaction of the organic with the static surface? Pointers to relevant articles or books would also be appreciated Rhanks Ronald Cook Principal Scientist TDA Research, Inc cookrl++tda.com From owner-chemistry@ccl.net Fri Apr 22 23:30:00 2011 From: "Roy Green powergreen : gmail.com" To: CCL Subject: CCL: Atom types of oplsaa force filed in Gaussian09 Message-Id: <-44457-110422232644-18034-ACTEdPKIE+sjYWLuH8VZ6A#,#server.ccl.net> X-Original-From: Roy Green Content-Type: multipart/alternative; boundary=bcaec5540a808e179704a18d8aff Date: Fri, 22 Apr 2011 21:26:33 -0600 MIME-Version: 1.0 Sent to CCL by: Roy Green [powergreen~~gmail.com] --bcaec5540a808e179704a18d8aff Content-Type: text/plain; charset=ISO-8859-1 Hi, All I am a beginner of molecular mechanics calculations. Can you help me decode the atom type symbols like MM1, MM2....in oplsaa force parameters that is implemented in G09. Those atom type indexes seem very different from other oplssa parameter format. Thank you in advance. Green --bcaec5540a808e179704a18d8aff Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi, All

I am a beginner of molecular mechanics calculations. Can you= help me decode the atom type symbols like MM1, MM2....in oplsaa force para= meters that is implemented in G09. Those atom type indexes seem very differ= ent from other oplssa parameter format.
Thank you in advance.

Green

=A0
--bcaec5540a808e179704a18d8aff--