1 Advances in Electronic Structure Theory: Gamess a Decade Later Mark S. Gordon and Michael W. Schmidt Department of Chemistry A
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Supporting Information
Electronic Supplementary Material (ESI) for RSC Advances. This journal is © The Royal Society of Chemistry 2020 Supporting Information How to Select Ionic Liquids as Extracting Agent Systematically? Special Case Study for Extractive Denitrification Process Shurong Gaoa,b,c,*, Jiaxin Jina,b, Masroor Abroc, Ruozhen Songc, Miao Hed, Xiaochun Chenc,* a State Key Laboratory of Alternate Electrical Power System with Renewable Energy Sources, North China Electric Power University, Beijing, 102206, China b Research Center of Engineering Thermophysics, North China Electric Power University, Beijing, 102206, China c Beijing Key Laboratory of Membrane Science and Technology & College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China d Office of Laboratory Safety Administration, Beijing University of Technology, Beijing 100124, China * Corresponding author, Tel./Fax: +86-10-6443-3570, E-mail: [email protected], [email protected] 1 COSMO-RS Computation COSMOtherm allows for simple and efficient processing of large numbers of compounds, i.e., a database of molecular COSMO files; e.g. the COSMObase database. COSMObase is a database of molecular COSMO files available from COSMOlogic GmbH & Co KG. Currently COSMObase consists of over 2000 compounds including a large number of industrial solvents plus a wide variety of common organic compounds. All compounds in COSMObase are indexed by their Chemical Abstracts / Registry Number (CAS/RN), by a trivial name and additionally by their sum formula and molecular weight, allowing a simple identification of the compounds. We obtained the anions and cations of different ILs and the molecular structure of typical N-compounds directly from the COSMObase database in this manuscript. -
GROMACS: Fast, Flexible, and Free
GROMACS: Fast, Flexible, and Free DAVID VAN DER SPOEL,1 ERIK LINDAHL,2 BERK HESS,3 GERRIT GROENHOF,4 ALAN E. MARK,4 HERMAN J. C. BERENDSEN4 1Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, S-75124 Uppsala, Sweden 2Stockholm Bioinformatics Center, SCFAB, Stockholm University, SE-10691 Stockholm, Sweden 3Max-Planck Institut fu¨r Polymerforschung, Ackermannweg 10, D-55128 Mainz, Germany 4Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, NL-9747 AG Groningen, The Netherlands Received 12 February 2005; Accepted 18 March 2005 DOI 10.1002/jcc.20291 Published online in Wiley InterScience (www.interscience.wiley.com). Abstract: This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simula- tions. The package includes about 100 utility and analysis programs. -
Chem Compute Quickstart
Chem Compute Quickstart Chem Compute is maintained by Mark Perri at Sonoma State University and hosted on Jetstream at Indiana University. The Chem Compute URL is https://chemcompute.org/. We will use Chem Compute as the frontend for running electronic structure calculations with The General Atomic and Molecular Electronic Structure System, GAMESS (http://www.msg.ameslab.gov/gamess/). Chem Compute also provides access to other computational chemistry resources including PSI4 and the molecular dynamics packages TINKER and NAMD, though we will not be using those resource at this time. Follow this link, https://chemcompute.org/gamess/submit, to directly access the Chem Compute GAMESS guided submission interface. If you are a returning Chem Computer user, please log in now. If your University is part of the InCommon Federation you can log in without registering by clicking Login then "Log In with Google or your University" – select your University from the dropdown list. Otherwise if this is your first time working with Chem Compute, please register as a Chem Compute user by clicking the “Register” link in the top-right corner of the page. This gives you access to all of the computational resources available at ChemCompute.org and will allow you to maintain copies of your calculations in your user “Dashboard” that you can refer to later. Registering also helps track usage and obtain the resources needed to continue providing its service. When logged in with the GAMESS-Submit tabs selected, an instruction section appears on the left side of the page with instructions for several different kinds of calculations. -
Popular GPU-Accelerated Applications
LIFE & MATERIALS SCIENCES GPU-ACCELERATED APPLICATIONS | CATALOG | AUG 12 LIFE & MATERIALS SCIENCES APPLICATIONS CATALOG Application Description Supported Features Expected Multi-GPU Release Status Speed Up* Support Bioinformatics BarraCUDA Sequence mapping software Alignment of short sequencing 6-10x Yes Available now reads Version 0.6.2 CUDASW++ Open source software for Smith-Waterman Parallel search of Smith- 10-50x Yes Available now protein database searches on GPUs Waterman database Version 2.0.8 CUSHAW Parallelized short read aligner Parallel, accurate long read 10x Yes Available now aligner - gapped alignments to Version 1.0.40 large genomes CATALOG GPU-BLAST Local search with fast k-tuple heuristic Protein alignment according to 3-4x Single Only Available now blastp, multi cpu threads Version 2.2.26 GPU-HMMER Parallelized local and global search with Parallel local and global search 60-100x Yes Available now profile Hidden Markov models of Hidden Markov Models Version 2.3.2 mCUDA-MEME Ultrafast scalable motif discovery algorithm Scalable motif discovery 4-10x Yes Available now based on MEME algorithm based on MEME Version 3.0.12 MUMmerGPU A high-throughput DNA sequence alignment Aligns multiple query sequences 3-10x Yes Available now LIFE & MATERIALS& LIFE SCIENCES APPLICATIONS program against reference sequence in Version 2 parallel SeqNFind A GPU Accelerated Sequence Analysis Toolset HW & SW for reference 400x Yes Available now assembly, blast, SW, HMM, de novo assembly UGENE Opensource Smith-Waterman for SSE/CUDA, Fast short -
Electronic Supporting Information a New Class of Soluble and Stable Transition-Metal-Substituted Polyoxoniobates: [Cr2(OH)4Nb10o
Electronic Supplementary Material (ESI) for Dalton Transactions This journal is © The Royal Society of Chemistry 2012 Electronic Supporting Information A New Class of Soluble and Stable Transition-Metal-Substituted Polyoxoniobates: [Cr2(OH)4Nb10O30]8-. Jung-Ho Son, C. André Ohlin and William H. Casey* A) Computational Results The two most interesting aspects of this new polyoxoanion is the inclusion of a more redox active metal and the optical activity in the visible region. For these reasons we in particular wanted to explore whether it was possible to readily and routinely predict the location of the absorbance bands of this type of compound. Also, owing to the difficulty in isolating the oxidised and reduced forms of the central polyanion dichromate species, we employed computations at the density functional theory (DFT) level to get a better idea of the potential characteristics of these forms. Structures were optimised for anti-parallel and parallel electronic spin alignments, and for both high and low spin cases where relevant. Intermediate spin configurations were 8- II III also tested for [Cr2(OH)4Nb10O30] . As expected, the high spin form of the Cr Cr complex was favoured (Table S1, below). DFT overestimates the bond lengths in general, but gives a good picture of the general distortion of the octahedral chromium unit, and in agreement with the crystal structure predicts that the shortest bond is the Cr-µ2-O bond trans from the central µ6- oxygen in the Lindqvist unit, and that the (Nb-)µ2-O-Cr-µ4-O(-Nb,Nb,Cr) angle is smaller by ca 5˚ from the ideal 180˚. -
Computer-Assisted Catalyst Development Via Automated Modelling of Conformationally Complex Molecules
www.nature.com/scientificreports OPEN Computer‑assisted catalyst development via automated modelling of conformationally complex molecules: application to diphosphinoamine ligands Sibo Lin1*, Jenna C. Fromer2, Yagnaseni Ghosh1, Brian Hanna1, Mohamed Elanany3 & Wei Xu4 Simulation of conformationally complicated molecules requires multiple levels of theory to obtain accurate thermodynamics, requiring signifcant researcher time to implement. We automate this workfow using all open‑source code (XTBDFT) and apply it toward a practical challenge: diphosphinoamine (PNP) ligands used for ethylene tetramerization catalysis may isomerize (with deleterious efects) to iminobisphosphines (PPNs), and a computational method to evaluate PNP ligand candidates would save signifcant experimental efort. We use XTBDFT to calculate the thermodynamic stability of a wide range of conformationally complex PNP ligands against isomeriation to PPN (ΔGPPN), and establish a strong correlation between ΔGPPN and catalyst performance. Finally, we apply our method to screen novel PNP candidates, saving signifcant time by ruling out candidates with non‑trivial synthetic routes and poor expected catalytic performance. Quantum mechanical methods with high energy accuracy, such as density functional theory (DFT), can opti- mize molecular input structures to a nearby local minimum, but calculating accurate reaction thermodynamics requires fnding global minimum energy structures1,2. For simple molecules, expert intuition can identify a few minima to focus study on, but an alternative approach must be considered for more complex molecules or to eventually fulfl the dream of autonomous catalyst design 3,4: the potential energy surface must be frst surveyed with a computationally efcient method; then minima from this survey must be refned using slower, more accurate methods; fnally, for molecules possessing low-frequency vibrational modes, those modes need to be treated appropriately to obtain accurate thermodynamic energies 5–7. -
Dalton2018.0 – Lsdalton Program Manual
Dalton2018.0 – lsDalton Program Manual V. Bakken, A. Barnes, R. Bast, P. Baudin, S. Coriani, R. Di Remigio, K. Dundas, P. Ettenhuber, J. J. Eriksen, L. Frediani, D. Friese, B. Gao, T. Helgaker, S. Høst, I.-M. Høyvik, R. Izsák, B. Jansík, F. Jensen, P. Jørgensen, J. Kauczor, T. Kjærgaard, A. Krapp, K. Kristensen, C. Kumar, P. Merlot, C. Nygaard, J. Olsen, E. Rebolini, S. Reine, M. Ringholm, K. Ruud, V. Rybkin, P. Sałek, A. Teale, E. Tellgren, A. Thorvaldsen, L. Thøgersen, M. Watson, L. Wirz, and M. Ziolkowski Contents Preface iv I lsDalton Installation Guide 1 1 Installation of lsDalton 2 1.1 Installation instructions ............................. 2 1.2 Hardware/software supported .......................... 2 1.3 Source files .................................... 2 1.4 Installing the program using the Makefile ................... 3 1.5 The Makefile.config ................................ 5 1.5.1 Intel compiler ............................... 5 1.5.2 Gfortran/gcc compiler .......................... 9 1.5.3 Using 64-bit integers ........................... 12 1.5.4 Using Compressed-Sparse Row matrices ................ 13 II lsDalton User’s Guide 14 2 Getting started with lsDalton 15 2.1 The Molecule input file ............................ 16 2.1.1 BASIS ................................... 17 2.1.2 ATOMBASIS ............................... 18 2.1.3 User defined basis sets .......................... 19 2.2 The LSDALTON.INP file ............................ 21 3 Interfacing to lsDalton 24 3.1 The Grand Canonical Basis ........................... 24 3.2 Basisset and Ordering .............................. 24 3.3 Normalization ................................... 25 i CONTENTS ii 3.4 Matrix File Format ................................ 26 3.5 The lsDalton library bundle .......................... 27 III lsDalton Reference Manual 29 4 List of lsDalton keywords 30 4.1 **GENERAL ................................... 31 4.1.1 *TENSOR ............................... -
Starting SCF Calculations by Superposition of Atomic Densities
Starting SCF Calculations by Superposition of Atomic Densities J. H. VAN LENTHE,1 R. ZWAANS,1 H. J. J. VAN DAM,2 M. F. GUEST2 1Theoretical Chemistry Group (Associated with the Department of Organic Chemistry and Catalysis), Debye Institute, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands 2CCLRC Daresbury Laboratory, Daresbury WA4 4AD, United Kingdom Received 5 July 2005; Accepted 20 December 2005 DOI 10.1002/jcc.20393 Published online in Wiley InterScience (www.interscience.wiley.com). Abstract: We describe the procedure to start an SCF calculation of the general type from a sum of atomic electron densities, as implemented in GAMESS-UK. Although the procedure is well known for closed-shell calculations and was already suggested when the Direct SCF procedure was proposed, the general procedure is less obvious. For instance, there is no need to converge the corresponding closed-shell Hartree–Fock calculation when dealing with an open-shell species. We describe the various choices and illustrate them with test calculations, showing that the procedure is easier, and on average better, than starting from a converged minimal basis calculation and much better than using a bare nucleus Hamiltonian. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 926–932, 2006 Key words: SCF calculations; atomic densities Introduction hrstuhl fur Theoretische Chemie, University of Kahrlsruhe, Tur- bomole; http://www.chem-bio.uni-karlsruhe.de/TheoChem/turbo- Any quantum chemical calculation requires properly defined one- mole/),12 GAMESS(US) (Gordon Research Group, GAMESS, electron orbitals. These orbitals are in general determined through http://www.msg.ameslab.gov/GAMESS/GAMESS.html, 2005),13 an iterative Hartree–Fock (HF) or Density Functional (DFT) pro- Spartan (Wavefunction Inc., SPARTAN: http://www.wavefun. -
Parameterizing a Novel Residue
University of Illinois at Urbana-Champaign Luthey-Schulten Group, Department of Chemistry Theoretical and Computational Biophysics Group Computational Biophysics Workshop Parameterizing a Novel Residue Rommie Amaro Brijeet Dhaliwal Zaida Luthey-Schulten Current Editors: Christopher Mayne Po-Chao Wen February 2012 CONTENTS 2 Contents 1 Biological Background and Chemical Mechanism 4 2 HisH System Setup 7 3 Testing out your new residue 9 4 The CHARMM Force Field 12 5 Developing Topology and Parameter Files 13 5.1 An Introduction to a CHARMM Topology File . 13 5.2 An Introduction to a CHARMM Parameter File . 16 5.3 Assigning Initial Values for Unknown Parameters . 18 5.4 A Closer Look at Dihedral Parameters . 18 6 Parameter generation using SPARTAN (Optional) 20 7 Minimization with new parameters 32 CONTENTS 3 Introduction Molecular dynamics (MD) simulations are a powerful scientific tool used to study a wide variety of systems in atomic detail. From a standard protein simulation, to the use of steered molecular dynamics (SMD), to modelling DNA-protein interactions, there are many useful applications. With the advent of massively parallel simulation programs such as NAMD2, the limits of computational anal- ysis are being pushed even further. Inevitably there comes a time in any molecular modelling scientist’s career when the need to simulate an entirely new molecule or ligand arises. The tech- nique of determining new force field parameters to describe these novel system components therefore becomes an invaluable skill. Determining the correct sys- tem parameters to use in conjunction with the chosen force field is only one important aspect of the process. -
D:\Doc\Workshops\2005 Molecular Modeling\Notebook Pages\Software Comparison\Summary.Wpd
CAChe BioRad Spartan GAMESS Chem3D PC Model HyperChem acd/ChemSketch GaussView/Gaussian WIN TTTT T T T T T mac T T T (T) T T linux/unix U LU LU L LU Methods molecular mechanics MM2/MM3/MM+/etc. T T T T T Amber T T T other TT T T T T semi-empirical AM1/PM3/etc. T T T T T (T) T Extended Hückel T T T T ZINDO T T T ab initio HF * * T T T * T dft T * T T T * T MP2/MP4/G1/G2/CBS-?/etc. * * T T T * T Features various molecular properties T T T T T T T T T conformer searching T T T T T crystals T T T data base T T T developer kit and scripting T T T T molecular dynamics T T T T molecular interactions T T T T movies/animations T T T T T naming software T nmr T T T T T polymers T T T T proteins and biomolecules T T T T T QSAR T T T T scientific graphical objects T T spectral and thermodynamic T T T T T T T T transition and excited state T T T T T web plugin T T Input 2D editor T T T T T 3D editor T T ** T T text conversion editor T protein/sequence editor T T T T various file formats T T T T T T T T Output various renderings T T T T ** T T T T various file formats T T T T ** T T T animation T T T T T graphs T T spreadsheet T T T * GAMESS and/or GAUSSIAN interface ** Text only. -
Kepler Gpus and NVIDIA's Life and Material Science
LIFE AND MATERIAL SCIENCES Mark Berger; [email protected] Founded 1993 Invented GPU 1999 – Computer Graphics Visual Computing, Supercomputing, Cloud & Mobile Computing NVIDIA - Core Technologies and Brands GPU Mobile Cloud ® ® GeForce Tegra GRID Quadro® , Tesla® Accelerated Computing Multi-core plus Many-cores GPU Accelerator CPU Optimized for Many Optimized for Parallel Tasks Serial Tasks 3-10X+ Comp Thruput 7X Memory Bandwidth 5x Energy Efficiency How GPU Acceleration Works Application Code Compute-Intensive Functions Rest of Sequential 5% of Code CPU Code GPU CPU + GPUs : Two Year Heart Beat 32 Volta Stacked DRAM 16 Maxwell Unified Virtual Memory 8 Kepler Dynamic Parallelism 4 Fermi 2 FP64 DP GFLOPS GFLOPS per DP Watt 1 Tesla 0.5 CUDA 2008 2010 2012 2014 Kepler Features Make GPU Coding Easier Hyper-Q Dynamic Parallelism Speedup Legacy MPI Apps Less Back-Forth, Simpler Code FERMI 1 Work Queue CPU Fermi GPU CPU Kepler GPU KEPLER 32 Concurrent Work Queues Developer Momentum Continues to Grow 100M 430M CUDA –Capable GPUs CUDA-Capable GPUs 150K 1.6M CUDA Downloads CUDA Downloads 1 50 Supercomputer Supercomputers 60 640 University Courses University Courses 4,000 37,000 Academic Papers Academic Papers 2008 2013 Explosive Growth of GPU Accelerated Apps # of Apps Top Scientific Apps 200 61% Increase Molecular AMBER LAMMPS CHARMM NAMD Dynamics GROMACS DL_POLY 150 Quantum QMCPACK Gaussian 40% Increase Quantum Espresso NWChem Chemistry GAMESS-US VASP CAM-SE 100 Climate & COSMO NIM GEOS-5 Weather WRF Chroma GTS 50 Physics Denovo ENZO GTC MILC ANSYS Mechanical ANSYS Fluent 0 CAE MSC Nastran OpenFOAM 2010 2011 2012 SIMULIA Abaqus LS-DYNA Accelerated, In Development NVIDIA GPU Life Science Focus Molecular Dynamics: All codes are available AMBER, CHARMM, DESMOND, DL_POLY, GROMACS, LAMMPS, NAMD Great multi-GPU performance GPU codes: ACEMD, HOOMD-Blue Focus: scaling to large numbers of GPUs Quantum Chemistry: key codes ported or optimizing Active GPU acceleration projects: VASP, NWChem, Gaussian, GAMESS, ABINIT, Quantum Espresso, BigDFT, CP2K, GPAW, etc. -
Dr. David Danovich
Dr. David Danovich ! 14 January 2021 (h-index: 34; 124 publications) Personal Information Name: Contact information Danovich David Private: Nissan Harpaz st., 4/9, Jerusalem, Date of Birth: 9371643 Israel June 29, 1959 Mobile: +972-54-4768669 E-mail: [email protected] Place of Birth: Irkutsk, USSR Work: Institute of Chemistry, The Hebrew Citizenship: University, Edmond Safra Campus, Israeli Givat Ram, 9190401 Jerusalem, Israel Marital status: Phone: +972-2-6586934 Married +2 FAX: +972-2-6584033 E-mail: [email protected] Current position 1992- present: Senior computational chemist and scientific programmer in the Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel Scientific skills Very experienced scientific researcher with demonstrated ability to implement ab initio molecular electronic structure and valence bond calculations for obtaining insights into physical and chemical properties of molecules and materials. Extensive expertise in implementation of Molecular Orbital Theory based on ab initio methods such as Hartree-Fock theory (HF), Density Functional Theory (DFT), Moller-Plesset Perturbation theory (MP2-MP5), Couple Cluster theories [CCST(T)], Complete Active Space (CAS, CASPT2) theories, Multireference Configuration Interaction (MRCI) theory and modern ab initio valence bond theory (VBT) methods such as Valence Bond Self Consistent Field theory (VBSCF), Breathing Orbital Valence Bond theory (BOVB) and its variants (like D-BOVB, S-BOVB and SD-BOVB), Valence Bond Configuration Interaction theory (VBCI), Valence Bond Perturbation theory (VBPT). Language skills Advanced Conversational English, Russian Hebrew Academic background 1. Undergraduate studies, 1978-1982 Master of Science in Physics, June 1982 Irkutsk State University, USSR Dr. David Danovich ! 2. Graduate studies, 1984-1989 Ph.