From owner-chemistry@ccl.net Wed Jan 11 05:58:01 2012 From: "Enrico D Ortenzio enrico.dortenzio,+,hotmail.it" To: CCL Subject: CCL: pure LDA calc in gaussview Message-Id: <-46140-120111055651-29387-uP6aqdJraeWRpjFrLF0hqg a server.ccl.net> X-Original-From: "Enrico D Ortenzio" Date: Wed, 11 Jan 2012 05:56:49 -0500 Sent to CCL by: "Enrico D Ortenzio" [enrico.dortenzio_+_hotmail.it] I'm doing tddft calculations on nickel compounds, but I noticed that among the dft functionals there is LSDA (including spin),but there is no lda. So I wanted to redo the lda calculation to see if spin affects the calculation or not, but there is no pure lda functional. there is a way to set it up gaussview ?(not sure if it is correct, but since LSDA is more useful for open-shell systems, in the settings I tried to do a restricted spin calculation using lsda .... but I don't know if it is correct) there is a way to set a pure lda calculation in gaussview or changing the input file manually? (g09w used for calculations) (sorry for bad english) Many thanks, Enrico D. p.s. : special thanks to Quartarolo Domenico From owner-chemistry@ccl.net Wed Jan 11 08:25:00 2012 From: "Tamas Gunda tgunda2!^!puma.unideb.hu" To: CCL Subject: CCL: What is the format of this file containing Cartesian coordinates? Message-Id: <-46141-120110073257-7640-2Z2evf40bvRHciCvbCNepA*|*server.ccl.net> X-Original-From: "Tamas Gunda" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Tue, 10 Jan 2012 13:32:47 +0100 MIME-Version: 1.0 Sent to CCL by: "Tamas Gunda" [tgunda2[#]puma.unideb.hu] Hi, Mol2Mol has been made just for the input of files with unknown formats. Any kind of format can be inputted with it using the appropriate format string. Look at: www.gunda.hu/mol2mol In this case copy the coordinates to the clipboard, open the file input window as general user input format, and create and select the following input format string: x y z d e d (this is for x y z coodinates, dummy, element symbol, dummy) and choose input from the clipboard The data are inputted. The molecule looks quite odd as apart from two OH groups all of the z coordinates of carbon atoms are nearly zero. Hope this helps Tamas Gunda -------------------------------------------------- > From: "Andrew DeYoung andrewdaviddeyoung- -gmail.com" Sent: Sunday, January 08, 2012 20:50 PM To: "Gunda, Gunda " Subject: CCL: What is the format of this file containing Cartesian coordinates? > > Sent to CCL by: Andrew DeYoung [andrewdaviddeyoung*|*gmail.com] > Hi, > > I have been reading the paper "Modeling of Graphite Oxide," > Boukhvalov, D. W.; Katsnelson, M. I., J. Am. Chem. Soc. 2008, 130, > 10697-10701. This paper has Supporting Information associated with > it, located here: http://pubs.acs.org/doi/suppl/10.1021/ja8021686 . > This Supporting Information contains the Cartesian coordinates for > various chemical species discussed in the paper (obtained by ab initio > calculations). For example, one of the series of coordinates that > this Supporting Information provides is the following: > > -0.02689401 0.05432733 1.07516282 3 H 1 > 0.03282702 -0.01179385 0.68330051 2 O 2 > 0.60586594 -0.05478650 -1.06215854 3 H 3 > 0.54625340 0.01126245 -0.67028541 2 O 4 > -0.00037430 0.00545262 0.11451905 1 C 5 > -0.87007097 0.50375034 -0.04749619 1 C 6 > -0.86607388 -0.50142967 -0.04692549 1 C 7 > 0.87536552 0.51049597 0.02025204 1 C 8 > 0.87795979 -0.51877321 0.02366501 1 C 9 > -0.00283324 1.00386837 -0.01257709 1 C 10 > 0.00039748 -1.00136092 -0.01066833 1 C 11 > -1.73307292 0.00197123 -0.03871588 1 C 12 > -0.86683173 1.50543512 -0.02856670 1 C 13 > -0.86909689 -1.50476823 -0.02691608 1 C 14 > 1.73809709 0.00167020 0.06437659 1 C 15 > 0.86891453 1.50286912 0.03907748 1 C 16 > 0.87181125 -1.50614862 0.04060303 1 C 17 > -1.73625671 1.00707540 -0.04218536 1 C 18 > -1.73743458 -1.00321958 -0.04099753 1 C 19 > 1.73948240 1.00519036 0.06254294 1 C 20 > 1.73748379 -1.00684011 0.06397068 1 C 21 > -0.00097315 2.00519687 -0.00474136 1 C 22 > -0.00025493 -2.00481803 -0.00256281 1 C 23 > -2.60679486 0.50744858 -0.05730558 1 C 24 > -2.60244033 -0.49997860 -0.05660149 1 C 25 > -1.73600183 2.00826255 -0.03828653 1 C 26 > -1.73589004 -2.00632024 -0.03581581 1 C 27 > -0.86809971 2.50743539 -0.01969374 1 C 28 > -0.86743107 -2.50800945 -0.01663035 1 C 29 > 1.73739025 -2.00803386 0.03602309 1 C 30 > 0.86918912 -2.50605556 0.01898868 1 C 31 > -2.60674237 1.50998962 -0.06149746 1 C 32 > -2.60337977 -1.50359739 -0.05952099 1 C 33 > -0.00151756 3.01254125 0.00026303 1 C 34 > -1.73833995 3.01353076 -0.04134158 1 C 35 > 1.73896850 -3.01089377 0.04144619 1 C 36 > -2.60747482 2.51319434 -0.06379837 1 C 37 > 0.87160242 -3.51651549 0.01963025 1 C 38 > -2.60959081 3.52137327 -0.06444686 1 C 39 > 1.74167046 -4.01903762 0.03732286 1 C 40 > 0.57935253 -0.00591929 -0.10150666 1 C 41 > -0.29895259 0.51824224 -0.01065610 1 C 42 > -0.29637000 -0.51095564 -0.00724144 1 C 43 > -1.15911004 -0.00215128 -0.05137018 1 C 44 > 0.57861451 1.00085598 0.02367761 1 C 45 > 0.58190077 -1.00453933 0.02559150 1 C 46 > -1.15848220 1.00634128 -0.05096692 1 C 47 > -1.16048708 -1.00566650 -0.04953595 1 C 48 > 1.44505788 0.50095217 0.05994684 1 C 49 > 1.44905447 -0.50423433 0.06052232 1 C 50 > -0.29287191 1.50575663 -0.02758935 1 C 51 > -0.28990959 -1.50337425 -0.02606221 1 C 52 > -2.02697593 0.50391544 -0.04217217 1 C 53 > -2.02491349 -0.50419505 -0.04152028 1 C 54 > 1.44809109 1.50425324 0.03991273 1 C 55 > 1.44587383 -1.50598582 0.04156281 1 C 56 > 0.57921418 2.00435850 0.01557045 1 C 57 > 0.58001551 -2.00575731 0.01775155 1 C 58 > -1.15838843 2.00756158 -0.02302302 1 C 59 > -1.15757535 -2.00795444 -0.02057379 1 C 60 > 2.31207394 -0.00245438 0.05172946 1 C 61 > -2.02776434 1.50719055 -0.04446594 1 C 62 > -2.02602610 -1.50572182 -0.04269775 1 C 63 > 2.31642963 1.00271453 0.05400912 1 C 64 > 2.31524228 -1.00755964 0.05519446 1 C 65 > -0.29021505 2.50557497 -0.00598370 1 C 66 > -0.28747789 -2.51054533 -0.00287556 1 C 67 > 1.44708230 -2.50791413 0.03270193 1 C 68 > 2.31499473 -2.00876451 0.05130262 1 C 69 > 0.58051995 -3.01303700 0.01275161 1 C 70 > -2.02771967 2.50972812 -0.04865231 1 C 71 > -1.15998355 3.01040245 -0.02842868 1 C 72 > 2.31732484 -3.01400623 0.05435683 1 C 73 > 1.45151430 -3.51897104 0.03339008 1 C 74 > -2.03208004 3.51717648 -0.04935652 1 C 75 > 2.31999134 -4.02068999 0.05257440 1 C 76 > > However, the Supporting Information (nor the article itself) appears > to specify the type of coordinate file that they are providing. For > example, is this in PDB format, XYZ format, or another format? Can > anyone please help me know which format this might be so that I can > save it in an appropriate file type and visualize the structure using > VMD? > > Thank you kindly! > > Andrew DeYoung > Carnegie Mellon University> > From owner-chemistry@ccl.net Wed Jan 11 09:59:00 2012 From: "mohamed med m.maatallah_+_ucam.ac.ma" To: CCL Subject: CCL:G: How to calculate ionization potential, electron affinity Message-Id: <-46142-120111061015-23969-y74AjLoSK1YhPTmF+gDonA++server.ccl.net> X-Original-From: "mohamed med" Date: Wed, 11 Jan 2012 06:10:13 -0500 Sent to CCL by: "mohamed med" [m.maatallah(~)ucam.ac.ma] dear collegues I am wondering How to calculate ionization potential, electron affinity and electro negativity values from Gaussian output files and suggest me the desired key word in order to calculate these values from output file. Thanks in advance From owner-chemistry@ccl.net Wed Jan 11 17:15:01 2012 From: "Joy Ku joyku~~stanford.edu" To: CCL Subject: CCL: Workshop:Rapid Molecular Dynamics Prototyping&Simulations with OpenMM Message-Id: <-46143-120111171207-23956-T6FsOQWKflgh2XxN0vk1zQ(a)server.ccl.net> X-Original-From: "Joy Ku" Date: Wed, 11 Jan 2012 17:12:05 -0500 Sent to CCL by: "Joy Ku" [joyku||stanford.edu] Simbios invites you to join us at its next Open Molecular Mechanics (OpenMM) workshop. OpenMM (http://simtk.org/home/openmm) is open-source software that enables molecular dynamics (MD) simulations to be accelerated on high performance computer architectures. It has demonstrated speed ups for both implicit solvent[1] and explicit solvent simulations[2] on graphics processing units (GPUs). And with the new application layer in its upcoming release, OpenMM will allow non-programmers to easily and quickly run MD simulations and develop custom algorithms on GPUs, while continuing to enable programmers to integrate OpenMM into their own programs. ***RAPID MOLECULAR DYNAMICS PROTOTYPING AND SIMULATIONS WITH OPENMM*** Where: Stanford University When: Feb. 16-17, 2012 Description: This workshop is designed for those interested in accelerating MD simulations on GPUs and/or developing new MD algorithms that can automatically be implemented and accelerated on GPUs. No programming background is required, though programming topics will also be covered for those who are interested in them. During the workshop, you will gain hands-on experience using OpenMMs new application layer and application programming interface (API). Learn to: * Set up and run an MD simulation on your GPU using both PDB and AMBER files * Create a custom force to apply to your simulations * Customize the simulation through Python scripting You will also have time to work with the OpenMM development team on your own research project. Registration is free but required and spaces are limited. To register or for more information, visit http://simbios.stanford.edu/MDWorkshops.htm. ________________________________________ OpenMM is 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., Efficient Nonbonded Interactions for Molecular Dynamics on a Graphics Processing Unit, J. Comp. Chem., 2010, 31(6):1268-1272.