Computational Chemistry for Chemistry Educators Shawn C
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Real-Time Pymol Visualization for Rosetta and Pyrosetta
Real-Time PyMOL Visualization for Rosetta and PyRosetta Evan H. Baugh1, Sergey Lyskov1, Brian D. Weitzner1, Jeffrey J. Gray1,2* 1 Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America, 2 Program in Molecular Biophysics, The Johns Hopkins University, Baltimore, Maryland, United States of America Abstract Computational structure prediction and design of proteins and protein-protein complexes have long been inaccessible to those not directly involved in the field. A key missing component has been the ability to visualize the progress of calculations to better understand them. Rosetta is one simulation suite that would benefit from a robust real-time visualization solution. Several tools exist for the sole purpose of visualizing biomolecules; one of the most popular tools, PyMOL (Schro¨dinger), is a powerful, highly extensible, user friendly, and attractive package. Integrating Rosetta and PyMOL directly has many technical and logistical obstacles inhibiting usage. To circumvent these issues, we developed a novel solution based on transmitting biomolecular structure and energy information via UDP sockets. Rosetta and PyMOL run as separate processes, thereby avoiding many technical obstacles while visualizing information on-demand in real-time. When Rosetta detects changes in the structure of a protein, new coordinates are sent over a UDP network socket to a PyMOL instance running a UDP socket listener. PyMOL then interprets and displays the molecule. This implementation also allows remote execution of Rosetta. When combined with PyRosetta, this visualization solution provides an interactive environment for protein structure prediction and design. Citation: Baugh EH, Lyskov S, Weitzner BD, Gray JJ (2011) Real-Time PyMOL Visualization for Rosetta and PyRosetta. -
An Explicit-Solvent Conformation Search Method Using Open Software
An explicit-solvent conformation search method using open software Kari Gaalswyk and Christopher N. Rowley Department of Chemistry, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada ABSTRACT Computer modeling is a popular tool to identify the most-probable conformers of a molecule. Although the solvent can have a large effect on the stability of a conformation, many popular conformational search methods are only capable of describing molecules in the gas phase or with an implicit solvent model. We have developed a work-flow for performing a conformation search on explicitly-solvated molecules using open source software. This method uses replica exchange molecular dynamics (REMD) to sample the conformational states of the molecule efficiently. Cluster analysis is used to identify the most probable conformations from the simulated trajectory. This work-flow was tested on drug molecules a-amanitin and cabergoline to illustrate its capabilities and effectiveness. The preferred conformations of these molecules in gas phase, implicit solvent, and explicit solvent are significantly different. Subjects Biophysics, Pharmacology, Computational Science Keywords Conformation search, Explicit solvent, Cluster analysis, Replica exchange molecular dynamics INTRODUCTION Many molecules can exist in multiple conformational isomers. Conformational isomers have the same chemical bonds, but differ in their 3D geometry because they hold different torsional angles (Crippen & Havel, 1988). The conformation of a molecule can affect Submitted 5 April 2016 chemical reactivity, molecular binding, and biological activity (Struthers, Rivier & Accepted 6May2016 Published 31 May 2016 Hagler, 1985; Copeland, 2011). Conformations differ in stability because they experience different steric, electrostatic, and solute-solvent interactions. The probability, p,ofa Corresponding author Christopher N. -
Python Tools in Computational Chemistry (And Biology)
Python Tools in Computational Chemistry (and Biology) Andrew Dalke Dalke Scientific, AB Göteborg, Sweden EuroSciPy, 26-27 July, 2008 “Why does ‘import numpy’ take 0.4 seconds? Does it need to import 228 libraries?” - My first Numpy-discussion post (paraphrased) Your use case isn't so typical and so suffers on the import time end of the balance. - Response from Robert Kern (Others did complain. Import time down to 0.28s.) 52,000 structures PDB doubles every 2½ years HEADER PHOTORECEPTOR 23-MAY-90 1BRD 1BRD 2 COMPND BACTERIORHODOPSIN 1BRD 3 SOURCE (HALOBACTERIUM $HALOBIUM) 1BRD 4 EXPDTA ELECTRON DIFFRACTION 1BRD 5 AUTHOR R.HENDERSON,J.M.BALDWIN,T.A.CESKA,F.ZEMLIN,E.BECKMANN, 1BRD 6 AUTHOR 2 K.H.DOWNING 1BRD 7 REVDAT 3 15-JAN-93 1BRDB 1 SEQRES 1BRDB 1 REVDAT 2 15-JUL-91 1BRDA 1 REMARK 1BRDA 1 .. ATOM 54 N PRO 8 20.397 -15.569 -13.739 1.00 20.00 1BRD 136 ATOM 55 CA PRO 8 21.592 -15.444 -12.900 1.00 20.00 1BRD 137 ATOM 56 C PRO 8 21.359 -15.206 -11.424 1.00 20.00 1BRD 138 ATOM 57 O PRO 8 21.904 -15.930 -10.563 1.00 20.00 1BRD 139 ATOM 58 CB PRO 8 22.367 -14.319 -13.591 1.00 20.00 1BRD 140 ATOM 59 CG PRO 8 22.089 -14.564 -15.053 1.00 20.00 1BRD 141 ATOM 60 CD PRO 8 20.647 -15.054 -15.103 1.00 20.00 1BRD 142 ATOM 61 N GLU 9 20.562 -14.211 -11.095 1.00 20.00 1BRD 143 ATOM 62 CA GLU 9 20.192 -13.808 -9.737 1.00 20.00 1BRD 144 ATOM 63 C GLU 9 19.567 -14.935 -8.932 1.00 20.00 1BRD 145 ATOM 64 O GLU 9 19.815 -15.104 -7.724 1.00 20.00 1BRD 146 ATOM 65 CB GLU 9 19.248 -12.591 -9.820 1.00 99.00 1 1BRD 147 ATOM 66 CG GLU 9 19.902 -11.351 -10.387 1.00 99.00 1 1BRD 148 ATOM 67 CD GLU 9 19.243 -10.169 -10.980 1.00 99.00 1 1BRD 149 ATOM 68 OE1 GLU 9 18.323 -10.191 -11.782 1.00 99.00 1 1BRD 150 ATOM 69 OE2 GLU 9 19.760 -9.089 -10.597 1.00 99.00 1 1BRD 151 ATOM 70 N TRP 10 18.764 -15.737 -9.597 1.00 20.00 1BRD 152 ATOM 71 CA TRP 10 18.034 -16.884 -9.090 1.00 20.00 1BRD 153 ATOM 72 C TRP 10 18.843 -17.908 -8.318 1.00 20.00 1BRD 154 ATOM 73 O TRP 10 18.376 -18.310 -7.230 1.00 20.00 1BRD 155 . -
The Norbornene Mystery Revealed
Supplementary Material (ESI) for Chemical Communications This journal is (c) The Royal Society of Chemistry 2010 Electronic Supporting Information The Norbornene Mystery Revealed Stephan N. Steinmann, Pierre Vogel, Yirong Mo, and Clémence Corminboeuf* To be published in Chemical Communication. The supplementary Data were prepared on June 22, 2010 and contains 14 pages. Contents: Method Section Figure S1: Molecules used for the comparisons between known experimental 1 Jcc-coupling constants (in Hertz) and the computed values. 1 Table S1 JCC-coupling comparison between experiment and computation. 1 Table S2: JCC-coupling constants for all compounds considered. Cartesian coordinates: B3LYP/6-311+G(d,p) (BLW and canonical) optimized structures for all compounds considered in the article. Contents: Computational Details 1 Table S1: JCC-coupling constants for all compounds considered. 1 Figure S1: Molecules for JCC-coupling comparison between experiment and computation. 1 Table S2: JCC-coupling comparison between experiment and computation. B3LYP/6-311+G(d,p) (BLW and canonical) optimized structures for all compounds considered in the article. Computational Details Standard geometries were optimized at the B3LYP1, 2/6-311+G** level using Gaussian 09.3 The BLW- constrained B3LYP/6-311+G** geometries (‘loc’) were optimized using a modified version of GAMESS-US (release 2008)4interfaced with the BLW-module.5, 6 Both the density and the J-coupling constants have been computed at the PBE7/IGLO-III level in Dalton 2.0.8 The BLW-eigenvalues and eigenvectors were optimized at the given DFT level with the SCF module of Dalton, SIRIUS, that has been interfaced with the BLW- module. -
Preparing and Analyzing Large Molecular Simulations With
Preparing and Analyzing Large Molecular Simulations with VMD John Stone, Senior Research Programmer NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign VMD Tutorials Home Page • http://www.ks.uiuc.edu/Training/Tutorials/ – Main VMD tutorial – VMD images and movies tutorial – QwikMD simulation preparation and analysis plugin – Structure check – VMD quantum chemistry visualization tutorial – Visualization and analysis of CPMD data with VMD – Parameterizing small molecules using ffTK Overview • Introduction • Data model • Visualization • Scripting and analytical features • Trajectory analysis and visualization • High fidelity ray tracing • Plugins and user-extensibility • Large system analysis and visualization VMD – “Visual Molecular Dynamics” • 100,000 active users worldwide • Visualization and analysis of: – Molecular dynamics simulations – Lattice cell simulations – Quantum chemistry calculations – Cryo-EM densities, volumetric data • User extensible scripting and plugins • http://www.ks.uiuc.edu/Research/vmd/ Cell-Scale Modeling MD Simulation VMD – “Visual Molecular Dynamics” • Unique capabilities: • Visualization and analysis of: – Trajectories are fundamental to VMD – Molecular dynamics simulations – Support for very large systems, – “Particle” systems and whole cells now reaching billions of particles – Cryo-EM densities, volumetric data – Extensive GPU acceleration – Quantum chemistry calculations – Parallel analysis/visualization with MPI – Sequence information MD Simulations Cell-Scale -
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. -
Car-Parrinello Molecular Dynamics
CPMD Car-Parrinello Molecular Dynamics An ab initio Electronic Structure and Molecular Dynamics Program The CPMD consortium WWW: http://www.cpmd.org/ Mailing list: [email protected] E-mail: [email protected] January 29, 2019 Send comments and bug reports to [email protected] This manual is for CPMD version 4.3.0 CPMD 4.3.0 January 29, 2019 Contents I Overview3 1 About this manual3 2 Citation 3 3 Important constants and conversion factors3 4 Recommendations for further reading4 5 History 5 5.1 CPMD Version 1.....................................5 5.2 CPMD Version 2.....................................5 5.2.1 Version 2.0....................................5 5.2.2 Version 2.5....................................5 5.3 CPMD Version 3.....................................5 5.3.1 Version 3.0....................................5 5.3.2 Version 3.1....................................5 5.3.3 Version 3.2....................................5 5.3.4 Version 3.3....................................6 5.3.5 Version 3.4....................................6 5.3.6 Version 3.5....................................6 5.3.7 Version 3.6....................................6 5.3.8 Version 3.7....................................6 5.3.9 Version 3.8....................................6 5.3.10 Version 3.9....................................6 5.3.11 Version 3.10....................................7 5.3.12 Version 3.11....................................7 5.3.13 Version 3.12....................................7 5.3.14 Version 3.13....................................7 5.3.15 Version 3.14....................................7 5.3.16 Version 3.15....................................8 5.3.17 Version 3.17....................................8 5.4 CPMD Version 4.....................................8 5.4.1 Version 4.0....................................8 5.4.2 Version 4.1....................................8 5.4.3 Version 4.3....................................9 6 Installation 10 7 Running CPMD 11 8 Files 12 II Reference Manual 15 9 Input File Reference 15 9.1 Basic rules........................................ -
Ab Initio Search for Novel Bxhy Building Blocks with Potential for Hydrogen Storage
Utah State University DigitalCommons@USU All Graduate Theses and Dissertations Graduate Studies 12-2010 Ab Initio Search for Novel BxHy Building Blocks with Potential for Hydrogen Storage Jared K. Olson Utah State University Follow this and additional works at: https://digitalcommons.usu.edu/etd Part of the Physical Chemistry Commons Recommended Citation Olson, Jared K., "Ab Initio Search for Novel BxHy Building Blocks with Potential for Hydrogen Storage" (2010). All Graduate Theses and Dissertations. 844. https://digitalcommons.usu.edu/etd/844 This Dissertation is brought to you for free and open access by the Graduate Studies at DigitalCommons@USU. It has been accepted for inclusion in All Graduate Theses and Dissertations by an authorized administrator of DigitalCommons@USU. For more information, please contact [email protected]. AB INITIO SEARCH FOR NOVEL BXHY BUILDING BLOCKS WITH POTENTIAL FOR HYDROGEN STORAGE by Jared K. Olson A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in Chemistry (Physical Chemistry) Approved: Dr. Alexander I. Boldyrev Dr. Steve Scheiner Major Professor Committee Member Dr. David Farrelly Dr. Stephen Bialkowski Committee Member Committee Member Dr. T.C. Shen Byron Burnham Committee Member Dean of Graduate Studies UTAH STATE UNIVERSITY Logan, Utah 2010 ii Copyright © Jared K. Olson 2010 All Rights Reserved iii ABSTRACT Ab Initio Search for Novel BxHy Building Blocks with Potential for Hydrogen Storage by Jared K. Olson, Doctor of Philosophy Utah State University, 2010 Major Professor: Dr. Alexander I. Boldyrev Department: Chemistry and Biochemistry On-board hydrogen storage presents a challenging barrier to the use of hydrogen as an energy source because the performance of current storage materials falls short of platform requirements. -
Surface Modification of Mgni by Perylene
Materials Transactions, Vol. 43, No. 11 (2002) pp. 2711 to 2716 Special Issue on Protium New Function in Materials c 2002 The Japan Institute of Metals Surface Modification of MgNi by Perylene Tiejun Ma, Yuji Hatano, Takayuki Abe and Kuniaki Watanabe Hydrogen Isotope Research Center, Toyama University, Toyama 930-8555, Japan Amorphous MgNi was modified by ball milling with perylene and its effects on the charge/discharge capacity were examined by using a conventional two-electrode cell. It was found that both the ball milling time and perylene/MgNi ratio had great influence on the discharge capacity and cycle life of MgNi. Three types of effects were identified, depending on ball-milling conditions. One of them was the increase in the discharge capacity at the first cycle, the second type was the deceleration of the degradation of the discharge capacity with charge/discharge cycle, and the last type was the reduction in the charge/discharge capacity. Chemical states of modified surfaces were analyzed by Auger electron spectroscopy (AES) as well as ab-inito calculation. Both AES and ab-initio calculations indicated that carbon atoms can form bonding with both magnesium and nickel atoms, but bonding with magnesium atoms is most preferable. The change in the charge/discharge capacity is attributed to such kind of reactions, and the three distinct effects are ascribed to the presence of different MgNi-perylene composites, formed during the ball milling on the surface, resulting in the retardation or acceleration of Mg(OH)2 formation on the electrode. (Received May 20, 2002; Accepted July 16, 2002) Keywords: magnesium, nickel, aromatic compound, surface modification, battery, electrode 1. -
Trends in Atomistic Simulation Software Usage [1.3]
A LiveCoMS Perpetual Review Trends in atomistic simulation software usage [1.3] Leopold Talirz1,2,3*, Luca M. Ghiringhelli4, Berend Smit1,3 1Laboratory of Molecular Simulation (LSMO), Institut des Sciences et Ingenierie Chimiques, Valais, École Polytechnique Fédérale de Lausanne, CH-1951 Sion, Switzerland; 2Theory and Simulation of Materials (THEOS), Faculté des Sciences et Techniques de l’Ingénieur, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland; 3National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland; 4The NOMAD Laboratory at the Fritz Haber Institute of the Max Planck Society and Humboldt University, Berlin, Germany This LiveCoMS document is Abstract Driven by the unprecedented computational power available to scientific research, the maintained online on GitHub at https: use of computers in solid-state physics, chemistry and materials science has been on a continuous //github.com/ltalirz/ rise. This review focuses on the software used for the simulation of matter at the atomic scale. We livecoms-atomistic-software; provide a comprehensive overview of major codes in the field, and analyze how citations to these to provide feedback, suggestions, or help codes in the academic literature have evolved since 2010. An interactive version of the underlying improve it, please visit the data set is available at https://atomistic.software. GitHub repository and participate via the issue tracker. This version dated August *For correspondence: 30, 2021 [email protected] (LT) 1 Introduction Gaussian [2], were already released in the 1970s, followed Scientists today have unprecedented access to computa- by force-field codes, such as GROMOS [3], and periodic tional power. -
Methods for the Refinement of Protein Structure 3D Models
International Journal of Molecular Sciences Review Methods for the Refinement of Protein Structure 3D Models Recep Adiyaman and Liam James McGuffin * School of Biological Sciences, University of Reading, Reading RG6 6AS, UK; [email protected] * Correspondence: l.j.mcguffi[email protected]; Tel.: +44-0-118-378-6332 Received: 2 April 2019; Accepted: 7 May 2019; Published: 1 May 2019 Abstract: The refinement of predicted 3D protein models is crucial in bringing them closer towards experimental accuracy for further computational studies. Refinement approaches can be divided into two main stages: The sampling and scoring stages. Sampling strategies, such as the popular Molecular Dynamics (MD)-based protocols, aim to generate improved 3D models. However, generating 3D models that are closer to the native structure than the initial model remains challenging, as structural deviations from the native basin can be encountered due to force-field inaccuracies. Therefore, different restraint strategies have been applied in order to avoid deviations away from the native structure. For example, the accurate prediction of local errors and/or contacts in the initial models can be used to guide restraints. MD-based protocols, using physics-based force fields and smart restraints, have made significant progress towards a more consistent refinement of 3D models. The scoring stage, including energy functions and Model Quality Assessment Programs (MQAPs) are also used to discriminate near-native conformations from non-native conformations. Nevertheless, there are often very small differences among generated 3D models in refinement pipelines, which makes model discrimination and selection problematic. For this reason, the identification of the most native-like conformations remains a major challenge. -
A Coarse-Grained Molecular Dynamics Simulation Using NAMD Package to Reveal Aggregation Profile of Phospholipids Self-Assembly in Water
Hindawi Publishing Corporation Journal of Chemistry Volume 2014, Article ID 273084, 6 pages http://dx.doi.org/10.1155/2014/273084 Research Article A Coarse-Grained Molecular Dynamics Simulation Using NAMD Package to Reveal Aggregation Profile of Phospholipids Self-Assembly in Water Dwi Hudiyanti,1 Muhammad Radifar,2 Tri Joko Raharjo,3 Narsito Narsito,3 and Sri Noegrohati4 1 Department of Chemistry, Diponegoro University, Jl. Prof. Sudharto, SH., Semarang 50257, Indonesia 2 Graduate School, Gadjah Mada University, Sekip Utara, Yogyakarta 55281, Indonesia 3 Department of Chemistry, FMIPA, Gadjah Mada University, Sekip Utara, Yogyakarta 55281, Indonesia 4 Faculty of Pharmacy, Gadjah Mada University, Sekip Utara, Yogyakarta 55281, Indonesia Correspondence should be addressed to Dwi Hudiyanti; dwi [email protected] Received 21 May 2014; Revised 11 July 2014; Accepted 14 July 2014; Published 4 August 2014 Academic Editor: Hugo Verli Copyright © 2014 Dwi Hudiyanti et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The energy profile of self-assembly process of DLPE, DLPS, DOPE, DOPS, DLiPE, and DLiPS in water was investigated by a coarse-grained molecular dynamics simulation using NAMD package. The self-assembly process was initiated from random configurations. The simulation was carried out for 160 ns. This study presented proof that there were three major self-assembled arrangements which became visible for a certain duration when the simulation took place, that is, liposome, deformed liposome, and planar bilayer. The energy profile that shows plateau at the time of these structures emerge confirmed their stability therein.