Lecture 2: Standard Software and Visualization Tools
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Introducing ONETEP: Linear-Scaling Density Functional Simulations on Parallel Computers Chris-Kriton Skylaris,A) Peter D
THE JOURNAL OF CHEMICAL PHYSICS 122, 084119 ͑2005͒ Introducing ONETEP: Linear-scaling density functional simulations on parallel computers Chris-Kriton Skylaris,a) Peter D. Haynes, Arash A. Mostofi, and Mike C. Payne Theory of Condensed Matter, Cavendish Laboratory, Madingley Road, Cambridge CB3 0HE, United Kingdom ͑Received 29 September 2004; accepted 4 November 2004; published online 23 February 2005͒ We present ONETEP ͑order-N electronic total energy package͒, a density functional program for parallel computers whose computational cost scales linearly with the number of atoms and the number of processors. ONETEP is based on our reformulation of the plane wave pseudopotential method which exploits the electronic localization that is inherent in systems with a nonvanishing band gap. We summarize the theoretical developments that enable the direct optimization of strictly localized quantities expressed in terms of a delocalized plane wave basis. These same localized quantities lead us to a physical way of dividing the computational effort among many processors to allow calculations to be performed efficiently on parallel supercomputers. We show with examples that ONETEP achieves excellent speedups with increasing numbers of processors and confirm that the time taken by ONETEP as a function of increasing number of atoms for a given number of processors is indeed linear. What distinguishes our approach is that the localization is achieved in a controlled and mathematically consistent manner so that ONETEP obtains the same accuracy as conventional cubic-scaling plane wave approaches and offers fast and stable convergence. We expect that calculations with ONETEP have the potential to provide quantitative theoretical predictions for problems involving thousands of atoms such as those often encountered in nanoscience and biophysics. -
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. -
Open Babel Documentation Release 2.3.1
Open Babel Documentation Release 2.3.1 Geoffrey R Hutchison Chris Morley Craig James Chris Swain Hans De Winter Tim Vandermeersch Noel M O’Boyle (Ed.) December 05, 2011 Contents 1 Introduction 3 1.1 Goals of the Open Babel project ..................................... 3 1.2 Frequently Asked Questions ....................................... 4 1.3 Thanks .................................................. 7 2 Install Open Babel 9 2.1 Install a binary package ......................................... 9 2.2 Compiling Open Babel .......................................... 9 3 obabel and babel - Convert, Filter and Manipulate Chemical Data 17 3.1 Synopsis ................................................. 17 3.2 Options .................................................. 17 3.3 Examples ................................................. 19 3.4 Differences between babel and obabel .................................. 21 3.5 Format Options .............................................. 22 3.6 Append property values to the title .................................... 22 3.7 Filtering molecules from a multimolecule file .............................. 22 3.8 Substructure and similarity searching .................................. 25 3.9 Sorting molecules ............................................ 25 3.10 Remove duplicate molecules ....................................... 25 3.11 Aliases for chemical groups ....................................... 26 4 The Open Babel GUI 29 4.1 Basic operation .............................................. 29 4.2 Options ................................................. -
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. -
The Alexandria Library, a Quantum-Chemical Database of Molecular Properties for Force field Development 9 2017 Received: October 1 1 1 Mohammad M
www.nature.com/scientificdata OPEN Data Descriptor: The Alexandria library, a quantum-chemical database of molecular properties for force field development 9 2017 Received: October 1 1 1 Mohammad M. Ghahremanpour , Paul J. van Maaren & David van der Spoel Accepted: 19 February 2018 Published: 10 April 2018 Data quality as well as library size are crucial issues for force field development. In order to predict molecular properties in a large chemical space, the foundation to build force fields on needs to encompass a large variety of chemical compounds. The tabulated molecular physicochemical properties also need to be accurate. Due to the limited transparency in data used for development of existing force fields it is hard to establish data quality and reusability is low. This paper presents the Alexandria library as an open and freely accessible database of optimized molecular geometries, frequencies, electrostatic moments up to the hexadecupole, electrostatic potential, polarizabilities, and thermochemistry, obtained from quantum chemistry calculations for 2704 compounds. Values are tabulated and where available compared to experimental data. This library can assist systematic development and training of empirical force fields for a broad range of molecules. Design Type(s) data integration objective • molecular physical property analysis objective Measurement Type(s) physicochemical characterization Technology Type(s) Computational Chemistry Factor Type(s) Sample Characteristic(s) 1 Uppsala Centre for Computational Chemistry, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden. Correspondence and requests for materials should be addressed to D.v.d.S. (email: [email protected]). -
![Automated Construction of Quantum–Classical Hybrid Models Arxiv:2102.09355V1 [Physics.Chem-Ph] 18 Feb 2021](https://docslib.b-cdn.net/cover/7378/automated-construction-of-quantum-classical-hybrid-models-arxiv-2102-09355v1-physics-chem-ph-18-feb-2021-177378.webp)
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. -
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. -
Natural Bond Orbital Analysis in the ONETEP Code: Applications to Large Protein Systems Louis P
WWW.C-CHEM.ORG FULL PAPER Natural Bond Orbital Analysis in the ONETEP Code: Applications to Large Protein Systems Louis P. Lee,*[a] Daniel J. Cole,[a] Mike C. Payne,[a] and Chris-Kriton Skylaris[b] First principles electronic structure calculations are typically Generalized Wannier Functions of ONETEP to natural atomic performed in terms of molecular orbitals (or bands), providing a orbitals, NBO analysis can be performed within a localized straightforward theoretical avenue for approximations of region in such a way that ensures the results are identical to an increasing sophistication, but do not usually provide any analysis on the full system. We demonstrate the capabilities of qualitative chemical information about the system. We can this approach by performing illustrative studies of large derive such information via post-processing using natural bond proteins—namely, investigating changes in charge transfer orbital (NBO) analysis, which produces a chemical picture of between the heme group of myoglobin and its ligands with bonding in terms of localized Lewis-type bond and lone pair increasing system size and between a protein and its explicit orbitals that we can use to understand molecular structure and solvent, estimating the contribution of electronic delocalization interactions. We present NBO analysis of large-scale calculations to the stabilization of hydrogen bonds in the binding pocket of with the ONETEP linear-scaling density functional theory package, a drug-receptor complex, and observing, in situ, the n ! p* which we have interfaced with the NBO 5 analysis program. In hyperconjugative interactions between carbonyl groups that ONETEP calculations involving thousands of atoms, one is typically stabilize protein backbones. -
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. -
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.