TDDFT As a Tool in Chemistry II
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MODELLER 10.1 Manual
MODELLER A Program for Protein Structure Modeling Release 10.1, r12156 Andrej Saliˇ with help from Ben Webb, M.S. Madhusudhan, Min-Yi Shen, Guangqiang Dong, Marc A. Martı-Renom, Narayanan Eswar, Frank Alber, Maya Topf, Baldomero Oliva, Andr´as Fiser, Roberto S´anchez, Bozidar Yerkovich, Azat Badretdinov, Francisco Melo, John P. Overington, and Eric Feyfant email: modeller-care AT salilab.org URL https://salilab.org/modeller/ 2021/03/12 ii Contents Copyright notice xxi Acknowledgments xxv 1 Introduction 1 1.1 What is Modeller?............................................. 1 1.2 Modeller bibliography....................................... .... 2 1.3 Obtainingandinstallingtheprogram. .................... 3 1.4 Bugreports...................................... ............ 4 1.5 Method for comparative protein structure modeling by Modeller ................... 5 1.6 Using Modeller forcomparativemodeling. ... 8 1.6.1 Preparinginputfiles . ............. 8 1.6.2 Running Modeller ......................................... 9 2 Automated comparative modeling with AutoModel 11 2.1 Simpleusage ..................................... ............ 11 2.2 Moreadvancedusage............................... .............. 12 2.2.1 Including water molecules, HETATM residues, and hydrogenatoms .............. 12 2.2.2 Changing the default optimization and refinement protocol ................... 14 2.2.3 Getting a very fast and approximate model . ................. 14 2.2.4 Building a model from multiple templates . .................. 15 2.2.5 Buildinganallhydrogenmodel -
Free and Open Source Software for Computational Chemistry Education
Free and Open Source Software for Computational Chemistry Education Susi Lehtola∗,y and Antti J. Karttunenz yMolecular Sciences Software Institute, Blacksburg, Virginia 24061, United States zDepartment of Chemistry and Materials Science, Aalto University, Espoo, Finland E-mail: [email protected].fi Abstract Long in the making, computational chemistry for the masses [J. Chem. Educ. 1996, 73, 104] is finally here. We point out the existence of a variety of free and open source software (FOSS) packages for computational chemistry that offer a wide range of functionality all the way from approximate semiempirical calculations with tight- binding density functional theory to sophisticated ab initio wave function methods such as coupled-cluster theory, both for molecular and for solid-state systems. By their very definition, FOSS packages allow usage for whatever purpose by anyone, meaning they can also be used in industrial applications without limitation. Also, FOSS software has no limitations to redistribution in source or binary form, allowing their easy distribution and installation by third parties. Many FOSS scientific software packages are available as part of popular Linux distributions, and other package managers such as pip and conda. Combined with the remarkable increase in the power of personal devices—which rival that of the fastest supercomputers in the world of the 1990s—a decentralized model for teaching computational chemistry is now possible, enabling students to perform reasonable modeling on their own computing devices, in the bring your own device 1 (BYOD) scheme. In addition to the programs’ use for various applications, open access to the programs’ source code also enables comprehensive teaching strategies, as actual algorithms’ implementations can be used in teaching. -
The Molecular Sciences Software Institute
The Molecular Sciences Software Institute T. Daniel Crawford, Cecilia Clementi, Robert Harrison, Teresa Head-Gordon, Shantenu Jha*, Anna Krylov, Vijay Pande, and Theresa Windus http://molssi.org S2I2 HEP/CS Workshop at NCSA/UIUC 07 Dec, 2016 1 Outline • Space and Scope of Computational Molecular Sciences. • “State of the art and practice” • Intellectual drivers • Conceptualization Phase: Identifying the community and needs • Bio-molecular Simulations (BMS) Conceptualization • Quantum Mechanics/Chemistry (QM) Conceptualization • Execution Phase. • Structure and Governance Model • Resource Distribution • Work Plan 2 The Molecular Sciences Software Institute (MolSSI) • New project (as of August 1st, 2016) funded by the National Science Foundation. • Collaborative effort by Virginia Tech, Rice U., Stony Brook U., U.C. Berkeley, Stanford U., Rutgers U., U. Southern California, and Iowa State U. • Total budget of $19.42M for five years, potentially renewable to ten years. • Joint support from numerous NSF divisions: Advanced Cyberinfrastructure (ACI), Chemistry (CHE), Division of Materials Research (DMR), Office of Multidisciplinary Activities (OMA) • Designed to serve and enhance the software development efforts of the broad field of computational molecular science. 3 Computational Molecular Sciences (CMS) • The history of CMS – the sub-fields of quantum chemistry, computational materials science, and biomolecular simulation – reaches back decades to the genesis of computational science. • CMS is now a “full partner with experiment”. • For an impressive array of chemical, biochemical, and materials challenges, our community has developed simulations and models that directly impact: • Development of new chiral drugs; • Elucidation of the functionalities of biological macromolecules; • Development of more advanced materials for solar-energy storage, technology for CO2 sequestration, etc. -
Basis Sets Running a Calculation • in Performing a Computational
Session 2: Basis Sets • Two of the major methods (ab initio and DFT) require some understanding of basis sets and basis functions • This session describes the essentials of basis sets: – What they are – How they are constructed – How they are used – Significance in choice 1 Running a Calculation • In performing a computational chemistry calculation, the chemist has to make several decisions of input to the code: – The molecular geometry (and spin state) – The basis set used to determine the wavefunction – The properties to be calculated – The type(s) of calculations and any accompanying assumptions 2 Running a calculation •For ab initio or DFT calculations, many programs require a basis set choice to be made – The basis set is an approx- imate representation of the atomic orbitals (AOs) – The program then calculates molecular orbitals (MOs) using the Linear Combin- ation of Atomic Orbitals (LCAO) approximation 3 Computational Chemistry Map Chemist Decides: Computer calculates: Starting Molecular AOs determine the Geometry AOs O wavefunction (ψ) Basis Set (with H H ab initio and DFT) Type of Calculation LCAO (Method and Assumptions) O Properties to HH be Calculated MOs 4 Critical Choices • Choice of the method (and basis set) used is critical • Which method? • Molecular Mechanics, Ab initio, Semiempirical, or DFT • Which approximation? • MM2, MM3, HF, AM1, PM3, or B3LYP, etc. • Which basis set (if applicable)? • Minimal basis set • Split-valence • Polarized, Diffuse, High Angular Momentum, ...... 5 Why is Basis Set Choice Critical? • The -
Multiscale Simulation of Laser Ablation and Processing of Semiconductor Materials
University of Central Florida STARS Electronic Theses and Dissertations, 2004-2019 2012 Multiscale Simulation Of Laser Ablation And Processing Of Semiconductor Materials Lalit Shokeen University of Central Florida Part of the Materials Science and Engineering Commons Find similar works at: https://stars.library.ucf.edu/etd University of Central Florida Libraries http://library.ucf.edu This Doctoral Dissertation (Open Access) is brought to you for free and open access by STARS. It has been accepted for inclusion in Electronic Theses and Dissertations, 2004-2019 by an authorized administrator of STARS. For more information, please contact [email protected]. STARS Citation Shokeen, Lalit, "Multiscale Simulation Of Laser Ablation And Processing Of Semiconductor Materials" (2012). Electronic Theses and Dissertations, 2004-2019. 2420. https://stars.library.ucf.edu/etd/2420 MULTISCALE SIMULATION OF LASER PROCESSING AND ABLATION OF SEMICONDUCTOR MATERIALS by LALIT SHOKEEN Bachelor of Science (B.Sc. Physics), University of Delhi, India, 2006 Masters of Science (M.Sc. Physics), University of Delhi, India, 2008 Master of Science (M.S. Materials Engg.), University of Central Florida, USA, 2009 A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Mechanical, Materials and Aerospace Engineering in the College of Engineering and Computer Science at the University of Central Florida Orlando, Florida, USA Fall Term 2012 Major Professor: Patrick Schelling © 2012 Lalit Shokeen ii ABSTRACT We present a model of laser-solid interactions in silicon based on an empirical potential developed under conditions of strong electronic excitations. The parameters of the interatomic potential depends on the temperature of the electronic subsystem Te, which is directly related to the density of the electron-hole pairs and hence the number of broken bonds. -
An Ab Initio Materials Simulation Code
CP2K: An ab initio materials simulation code Lianheng Tong Physics on Boat Tutorial , Helsinki, Finland 2015-06-08 Faculty of Natural & Mathematical Sciences Department of Physics Brief Overview • Overview of CP2K - General information about the package - QUICKSTEP: DFT engine • Practical example of using CP2K to generate simulated STM images - Terminal states in AGNR segments with 1H and 2H termination groups What is CP2K? Swiss army knife of molecular simulation www.cp2k.org • Geometry and cell optimisation Energy and • Molecular dynamics (NVE, Force Engine NVT, NPT, Langevin) • STM Images • Sampling energy surfaces (metadynamics) • DFT (LDA, GGA, vdW, • Finding transition states Hybrid) (Nudged Elastic Band) • Quantum Chemistry (MP2, • Path integral molecular RPA) dynamics • Semi-Empirical (DFTB) • Monte Carlo • Classical Force Fields (FIST) • And many more… • Combinations (QM/MM) Development • Freely available, open source, GNU Public License • www.cp2k.org • FORTRAN 95, > 1,000,000 lines of code, very active development (daily commits) • Currently being developed and maintained by community of developers: • Switzerland: Paul Scherrer Institute Switzerland (PSI), Swiss Federal Institute of Technology in Zurich (ETHZ), Universität Zürich (UZH) • USA: IBM Research, Lawrence Livermore National Laboratory (LLNL), Pacific Northwest National Laboratory (PNL) • UK: Edinburgh Parallel Computing Centre (EPCC), King’s College London (KCL), University College London (UCL) • Germany: Ruhr-University Bochum • Others: We welcome contributions from -
Automated Construction of Quantum–Classical Hybrid Models Arxiv:2102.09355V1 [Physics.Chem-Ph] 18 Feb 2021
Automated construction of quantum{classical hybrid models Christoph Brunken and Markus Reiher∗ ETH Z¨urich, Laboratorium f¨urPhysikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Z¨urich, Switzerland February 18, 2021 Abstract We present a protocol for the fully automated construction of quantum mechanical-(QM){ classical hybrid models by extending our previously reported approach on self-parametri- zing system-focused atomistic models (SFAM) [J. Chem. Theory Comput. 2020, 16 (3), 1646{1665]. In this QM/SFAM approach, the size and composition of the QM region is evaluated in an automated manner based on first principles so that the hybrid model describes the atomic forces in the center of the QM region accurately. This entails the au- tomated construction and evaluation of differently sized QM regions with a bearable com- putational overhead that needs to be paid for automated validation procedures. Applying SFAM for the classical part of the model eliminates any dependence on pre-existing pa- rameters due to its system-focused quantum mechanically derived parametrization. Hence, QM/SFAM is capable of delivering a high fidelity and complete automation. Furthermore, since SFAM parameters are generated for the whole system, our ansatz allows for a con- venient re-definition of the QM region during a molecular exploration. For this purpose, a local re-parametrization scheme is introduced, which efficiently generates additional clas- sical parameters on the fly when new covalent bonds are formed (or broken) and moved to the classical region. arXiv:2102.09355v1 [physics.chem-ph] 18 Feb 2021 ∗Corresponding author; e-mail: [email protected] 1 1 Introduction In contrast to most protocols of computational quantum chemistry that consider isolated molecules, chemical processes can take place in a vast variety of complex environments. -
ORGANIZATION of BIOMOLECULES in a 3-DIMENSIONAL SPACE by Sameer Sajja a Thesis Submitted to the Faculty of the University Of
ORGANIZATION OF BIOMOLECULES IN A 3-DIMENSIONAL SPACE by Sameer Sajja A thesis submitted to the faculty of The University of North Carolina at Charlotte in partial fulfillment of the requirements for the degree of Master of Science in Chemistry Charlotte 2019 Approved by: ________________________________ Dr. Kirill Afonin ________________________________ Dr. Caryn Striplin ________________________________ Dr. Joanna Krueger ________________________________ Dr. Yuri Nesmelov ii ©2019 Sameer Sajja ALL RIGHTS RESERVED iii ABSTRACT SAMEER SAJJA. Organization of Biomolecules in a 3-Dimensional Space (Under the direction of DR. KIRILL A. AFONIN) The human body operates using various stimuli-responsive mechanisms, dictating biological activity via reaction to external cues. Hydrogels are networked hydrophilic polymeric materials that offer the potential to recreate aqueous environments with controlled organization of biomolecules for research purposes and potential therapeutic use. The unique, programmable structure of hydrogels exhibit similar physicochemical properties to those of living tissues while also introducing component-mediated biocompatibility. The design of stimuli-responsive biocompatible hydrogels would further allow for controllable mechanical and functional properties tuned by changes in environmental factors. This study investigates individual biomolecular components needed to potentially engineer biocompatible and stimuli-responsive hydrogels. By utilizing programmable biomolecules such as nucleic acids (DNA and RNA) and proteins -
Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development
processes Review Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development Outi M. H. Salo-Ahen 1,2,* , Ida Alanko 1,2, Rajendra Bhadane 1,2 , Alexandre M. J. J. Bonvin 3,* , Rodrigo Vargas Honorato 3, Shakhawath Hossain 4 , André H. Juffer 5 , Aleksei Kabedev 4, Maija Lahtela-Kakkonen 6, Anders Støttrup Larsen 7, Eveline Lescrinier 8 , Parthiban Marimuthu 1,2 , Muhammad Usman Mirza 8 , Ghulam Mustafa 9, Ariane Nunes-Alves 10,11,* , Tatu Pantsar 6,12, Atefeh Saadabadi 1,2 , Kalaimathy Singaravelu 13 and Michiel Vanmeert 8 1 Pharmaceutical Sciences Laboratory (Pharmacy), Åbo Akademi University, Tykistökatu 6 A, Biocity, FI-20520 Turku, Finland; ida.alanko@abo.fi (I.A.); rajendra.bhadane@abo.fi (R.B.); parthiban.marimuthu@abo.fi (P.M.); atefeh.saadabadi@abo.fi (A.S.) 2 Structural Bioinformatics Laboratory (Biochemistry), Åbo Akademi University, Tykistökatu 6 A, Biocity, FI-20520 Turku, Finland 3 Faculty of Science-Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands; [email protected] 4 Swedish Drug Delivery Forum (SDDF), Department of Pharmacy, Uppsala Biomedical Center, Uppsala University, 751 23 Uppsala, Sweden; [email protected] (S.H.); [email protected] (A.K.) 5 Biocenter Oulu & Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7 A, FI-90014 Oulu, Finland; andre.juffer@oulu.fi 6 School of Pharmacy, University of Eastern Finland, FI-70210 Kuopio, Finland; maija.lahtela-kakkonen@uef.fi (M.L.-K.); tatu.pantsar@uef.fi -
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˚. -
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. -
Implementation of Methods to Accurately Predict Transition Pathways and the Underlying Potential Energy Surface of Biomolecular Systems
IMPLEMENTATION OF METHODS TO ACCURATELY PREDICT TRANSITION PATHWAYS AND THE UNDERLYING POTENTIAL ENERGY SURFACE OF BIOMOLECULAR SYSTEMS By DELARAM GHOREISHI A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2019 c 2019 Delaram Ghoreishi I dedicate this dissertation to my mother, my brother, and my partner. For their endless love, support, and encouragement. ACKNOWLEDGMENTS I am thankful to my advisor, Adrian Roitberg, for his guidance during my graduate studies. I am grateful for the opportunities he provided me and for allowing me to work independently. I also thank my committee members, Rodney Bartlett, Xiaoguang Zhang, and Alberto Perez, for their valuable inputs. I am grateful to the University of Florida Informatics Institue for providing financial support in 2016, allowing me to take a break from teaching and focus more on research. I like to acknowledge my group members and friends for their moral support and technical assistance. Natali di Russo helped me become familiar with Amber. I thank Pilar Buteler, Sunidhi Lenka, and Vinicius Cruzeiro for daily conversations regarding science and life. Pancham Lal Gupta was my cpptraj encyclopedia. I thank my physicist colleagues, Ankita Sarkar and Dustin Tracy, who went through the intense physics coursework with me during the first year. I thank Farhad Ramezanghorbani, Justin Smith, Kavindri Ranasinghe, and Xiang Gao for helpful discussions regarding ANI and active learning. I also thank David Cerutti from Rutgers University for his help with NEB implementation. I thank Pilar Buteler and Alvaro Gonzalez for the good times we had camping and climbing.