Masa Katagiri: Scientific Programs and Links

Masa Katagiri

Scientific Programs and Links

If you have more information, please send me mail. Email: katagiri@nrim.go.jp

Constants
- Conversion of Units
- Fundamental Physical Constants
- Physical Constants and Astronomical Data
Ab Initio Programs
- 2D - Numerical Hartree-Fock Program for Diatomic Molecules
- CRYSTAL
- COLUMBUS
- GAMESS
- HyperChem
- mopac7
- MESSKit
- MOTECC-91
- PSI 2.0 - PSI is capable of evaluating SCF, MCSCF, CI, CCSD, and CCSD(T) wavefunctions and analytical gradients using expansions over Gaussian type orbitals.
- SYMOL program package - Restricted Open Shell Hartree Fock program
- Turbomole - TURBOMOLE is a program package for ab initio electronic structure calculations - mainly on the SCF level of theory - which is especially designed to be used on workstation computers. It has already been applied to molecules containing more than 100 atoms.
- Augmented Spherical Wave method (ASW) by Volker Eyert
Density Functional Programs
- ACRES - Adaptive Coordinate Real-space Electronic Structure code: ACRES is a density-functional theory (DFT) code designed to perform total energy calculations for atoms, molecules, bulk solids and surfaces on parallel computers such as CM-5, IBM SP2 and ORIGIN 2000. These calculations are performed in real space on a grid that is adapted to spatially inhomogeneous cutoff (or resolution) requirements of a given system. Sparsity of the DFT Kohn-Sham hamiltonian in real space and load balancing resulting from the adaptive mesh make ACRES an excellent technique for use on parallel computers. It can be used to perform all-electron calculations for the above systems, though most practical applications to crystalline solids involve using pseudopotentials to represent the interaction between nuclei and electrons. ACRES also computes Hellman-Feynman forces acting on atoms allowing relaxation of structures.
- ADF - ADF is the Amsterdam Density Functional program system for electronic structure calculations.
- CASTEP - CASTEP is an ab initio code for the solution of the electronic ground state of periodic systems with the wavefunctions expanded in a PW basis using a technique based on density functional theory. The CETEP code is similar to CASTEP but designed to run on massively parallel supercomputers. This latter code was developed as part of the UKCP collaboration.
- BDF - Beijing 4-component density-functional program package (relativistic DFT)
- DeFT
- DoD-Planewave: A General Scalable Density Functional Code
- GAUSSIAN-94
- PS-GVB
- Q-Chem
- Spartan
- TB-LMTO -The development of this program has been managed by Ole Krogh Andersen; the first version was constructed mostly by Mark van Schilfgaarde Schilfgaarde during 1987-88. Over the years the following people (in alphabetic order) have written, corrected or made additions to the program: Vladimir Antonov (e-mail address in Ukraine is anton%d24imp.kiev.ua@relay.eunet.fi), Peter Braun, Armin Burkhardt, Volker Eyert, Ove Jepsen, Georges Krier, Toni A. Paxton, Andrei Postnikov, and Andreas Savin.
- WIEN97 - A Full Potential LAPW Package for Calculating Crystal Properties
Quantum Molecular Dynamics, Car-Parrinello Methods
- CPMD - stuttgart Parinello's group
- fhi93cp - Car-Parinello MD-program
- JEEP - A free, easy to use first-principles electronic structure program.
Basis Sets
- DGauss Basis Sets
- Gaussian Basis Set Order Form
- MOLPRO Basis Set Library
Pseudopotentials
- Psudopotential - ECP
- Energy-Consistent Pseudopotentials of the Stuttgart Group
- J. L. Martins - Pseudopotentlal Generator
- NCPS - Pseudopotentlal Generator
Crystallography Programs
- Frodo-TOM
- SIR92
- SIRPOW.92
Desktop Publishing and Molecular Modeling
- Accord
- Accord Internet Chemistry Viewer
- Cambridge Scientific - ChemDraw
- Chemistry 4-D Draw
- ISIS/Draw
- SoftShell
Useful Programs for Molecular Dynamics
- Particle Mesh Ewald (PME) method
- fractional coordinates
Modeling
- AccuModel
- AMBER
- AMBER, Cornell et al. 1995 AMBER force field
- BioModel
- BioPad
- Galaxy
- HASL
- HINT
- HINT
- HyperChem
- MacroModel
- MODELLER european miiror
- Modeller
- Mol2D
- Molgen
- MOLVIB
- NAMOT
- NAOMI
- Nucleic Acid Structure Analysis
- ORTEP
- pallas
- PDM93
- Procheck
- RASSE
- Ryuga - For 3-Dimensional Dynamic Visualization of the Molecular Dynamics Calculation Result with Virtual Reality
- Sculpt
- Solid State Simulation (SSS) Project
- UniChem
- Spartan
- TINKER
- WHAT IF - versatile protein structure analysis program
Molecular Dynamics and Mechanics Programs
- charmm
- dl_poly
- GROMACS
- GROMOS
- MARVIN
- MM3
- moil
- Moldy
- MOLSCAT
- MORATE
- NAMD
- PIMM - Pi-SCF-Molecular Mechanics Program
- POLYRATE
- SCARECROW
Nomenclature
- Autonom
- ACD/Name
- SMILES
NMR Processing and Prediction
- ACD/CNMR
- GAMMA
- GIFA
- ACD/HNMR
- MestRe-C
- MORASS
- NUTS
- SwaN-MR
Molecular and Scientific Visualization
- CACAO
- CASCADE
- Chemscape Chime
- Eadfrith
- Geomview
- Gifa
- JCAMP-DX Conversion Program
- jmr_bs
- MDH - MDRANGE (MDH) program
- MOIL-View
- MolEdit
- molgen
- MOLMOL
- moplot2
- Moviemol
- PSI88 Molecular Orbital Plotting Package
- psi88
- RasMol
- rasmol2
- SciAn
- Spartan
- Steric
- UniChem
- VChem
- Viewmol - Viewmol is a graphical front end for computational chemistry programs. It is able to graphically aid in the generation of molecular structures for computations and to visualize their results.
- WebLab Viewer
- XMol
Polymer
- Threader
Poisson-Boltzmann quation
- DelPhi
Potential Functions and Databases
- AMBER
- Royal Institution Potentials Library: Index
- spline fitting routines for various kinds of data and geometries
Semiempirical Programs
- AMPAC 6.0
- AMSOL
- Argus
- HyperChem
- SIBIQ
Tight Binding
- DoD-Parallel Tight-Binding Molecular Dynamics
- Genetic Algorithms and LCAO parameters
- Tight-Binding parameters periodic table
- YAeHMOP
- znew3
- Huckel
Misc. Programs
- Calaco (a unit coonversion tool)
- Ciara (a reaction planning tool)
- MOE (Molecular Operating Environment)
- QuikTag (a reference manager)
Data Analysis and Conversion Programs
- Babel
- PreQuest
- O-Matrix
Other Links for Scientific Programs
- Lawless Research Group at the University of Sussex
- Netlib - Netlib is a collection of mathematical software, papers, and databases.
- Oxford Molecular Products
- QSAR Server - Quantitative Structure-Activity Relationships Server at UNC Chapel Hill
- Modelado Molecular
- ANTAS - THE MOLECULAR MODELING RESEARCH GROUP
Useful subroutines
- SLALIB - Positional Astronomy Library
- Los Alamos - CLAMS routines
- AIX Version 4 Technical Reference, Volume 2: Base Operating System and Extensions
- CN/ASD group documentation
- MERLIN-3.0, A multidimensional optimization environment. - MERLIN provides a programmable environment that makes the whole process of minimizing multidimensional function with bound constraints, flexible and efficient. Ten algorithms and a strategy are implemented. Two of them use only function values, while the rest use gradient information as well. One algorithm is specific for functions that can be cast in a sum of squares form. (CPC ADHQ)
- The MERLIN control language for strategic optimization. - This special purpose language is built to allow the user to devise successful and efficient strategies based on diverse algorithmic approaches, in a systematic and orderly manner, using the MERLIN optimization environment. (CPC ADHR)
- Minuit - minimization package
Databases
- CCDC - Cambridge Crystallographic Data Centre
- ChemFinder Searching
- CHIRBASE MOLECULAR DATABASE FOR CHIRAL CHROMATOGRAPHY
- ChemKey Search Database
- CODATA
- CrossFire
- Daylight Chemical Information Systems
- Crystal Structure
- General Physics Research Center
- DIELECTRIC CONSTANT REFERENCE GUIDE - ASI Instruments Inc.
- ESF - Department of Chemistry, SUNY-ESF, Syracuse, NY.
- Fetch and Sketch
- Fluorescent Chemosensors and Biosensors Database
- Gaussian Basis Set Order Form
- Materials Science Database - band structure, binding energy, cluster ...
- Molecular Database Query
- NIST Chemistry WebBook
- PDB - Protein Data Bank
- Psudopotential - ECP
- Three-Dimensional Drug Structure Databank
- WWW Chemical Structures Database
Protein Databank
- Protein Data Bank - Brookhaven national laboratory
- ATLAS of Nucleic Acid Containing Structure - he Nucleic Acid Database Project, Rutgers, The State University of New Jersey
Periodic Tebles
- Periodic Table - Los Alamos National Laboratory
- Yinon Bentor's Periodic Table
- Chemicool
- X-ray Properties
- Periodic Table
- Periodic Table - WebElements
- Element
- WebElements
- Periodic Table Software for Windows
Reference Search
- Chemical Abstracts Service: A Scientific Information Resource
- BIDS
- MELVYL
- MELVYL - Current Contentsｮ on MELVYLｮ
- Current Contents Journals included in Physical, Chemical & Earth Sciences
- QUB Library Search
- xxx abstruct search
Integrated Graphics Systems
- Integrated Graphics Systems
Academic Societies
- American Chemical Society
Molecular Simulations, Inc.
- Home Page
- SDK
- New science@msi resource
Home Pages
- Advanced Computing Laboratory - ACL
- CambridgeSoft Corporation,
- ChemWeb
- Collaborative Computational - CCP
- CCP5 - The computer simulation by molecular dynamics, monte carlo and molecular mechanics of liquid and solid phases.
- Colorado State University, Chemistry Department
- Complex Systems Theory Branch, Code 6690
- Computational Chemistry List - CCL
- Daresbury Laboratory - CCLRC
- Gaussian, Inc.
- JRCAT
- Kaxiras Group
- MolSoft
- Max-Planck Institute Stuttgart
- Molecular Dynamics, Inc.
- Molecular Monte Carlo - MMC
- MRS: Materials Research Society
- National Research Council of Canada's (NRC's) Steacie Institute for Molecular Sciences (SIMS)
- Netwaork Science - NetSci
- Numerical Recipes
- NIU Chemistry WWW Site
- Oxford Molecular Solutions for Discovery Research
- RITE
- Structural Bioinformatics, Inc.
- Supercomputer Centers
- TCI software research
- WWW Chemicals
- WWW Virtual Library: Technical Ceramics
Home Pages - Universities etc.
- CECAM - European Centre for Atomic and Molecular Computations
- Cambridge University, Department of Chemistry
- Cambridge University, Department of Materials Science and Metallurgy
- Cambridge University, Department of Physics, Cavendish Laboratory
- Hirosaki University
- Hirosaki University - Dept of Materials Science and Technology
- Hiroshima University - Science
- Ibaraki University
- Japanese Universities - list of sites
- Kyoto University
- National Research Institute for Metals - NRIM
- Okayama University - Dept of Physics
- Oxford University
- Oxford University - Department of Materials
- Oxford University - Materials Modelling Laboratory (MML)
- Shizuoka University - Kogakubu, System Eng
- Tokyo University
- Tohoku University
- Tohoku University, Institute for Advanced Materials Processing - IAMP (Sozai Kougaku Kenkyujo)
- Tohoku University, Miyamoto lab
- Tohoku University, Tanaka lab
- Trinity College Dublin, Physics
- University College London, Dept. Physics and Astronomy, CONDENSED MATTER & MATERIALS PHYSICS
- Universities in UK
- Universities of Toronto - Chemistry Dept
Academic Societies
- Computational Chemistry and Materials Science (CCM)
- Japanese Academic Societiy Page List
- Chemical Society of Japan - Nihon Kagaku Kai
- Japan Institute of Metals - Kinzoku Gakkai
- Physical Society of Japan - Nihon Butsuri Gakkai
Publishers & Book Shops
- Amazon, Search by Keyword
- Cambridge University Press, Physics
- Gordon and Breach Science Publishers
- Gordon and Breach Science Publishers - registration
- Elsevier Science
- Marcel Dekker
- Oxford University Press U.S.A. - OUP Catalog Index
ARTICLES ONLINE
- American Institute of Physics - Tables of Contents (and abstracts for some journals) are available for browsing by all users. Downloading of full-text articles requires a subscription to the publication. Document delivery services are available to non-subscribers.
- ChemWeb - Elsevier Science titles are available through ChemWeb by using Associated-Personal Subscriptions
- Elsevier Science
- IOP - Institute of Physics
- Gordon and Breach Publishing Group
Journals
- Accounts of Chemical Research
- Applied Catalysis A: General
- Applied Catalysis B: Environmental
- Biochemistry
- Bulletin of the Chemical Society of Japan
- Catalysis Today
- Chemical Physics Letters
- Chemical Reviews
- Computational Materials Science
- Computer Physics Communications - CPC Program Library
- Computers in Physics
- Dalton Transactions
- Electronic Journal of Theoretical Chemistry
- Faraday Transactions
- Inorganic Chemistry
- Japanese Journal of Applied Physics - JJAP
- JETP Letters
- Journal of Computer-Aided Molecular Design
- Journal of Molecular Catalysis A: Chemical
- Journal of Molecular Catalysis B: Enzymatic
- Journal of Molecular Modeling
- Journal of American Chemical Society
- Journal of Biological Chemistry
- Journal of Chemical Physics
- Journal of Computational Chemistry
- Journal of Molecular Biology
- Journal of Molecular Spectroscopy
- Journal of Molecular Structure
- Journal of Molecular Structure: Theochem
- Journal of Organic Chemistry
- Journal of Physical Chemistry
- Journal of Physics A: Mathematical and General
- Journal of Physics B: Atomic, Molecular and Optical Physics
- Journal of Physics: Condensed Matter
- Journal of Physics D: Applied Physics
- Journal of Physics G: Nuclear and Particle Physics
- Journal of Supercritical Fluids
- Microporous and Mesoporous Materials
- Modelling and Simulation in Materials Science and Engineering
- Molecular Simulation
- Nature　
- Organometallics
- Perkin Transactions 1
- Perkin Transactions 2
- Physica C: Superconductivity
- Physical Review
- Physical Review A
- Physical Review B
- Physical Review B Rapid Communications
- Physical Review C
- Physical Review D
- Physical Review E
- Physical Review Letters
- Physics of Solid State
- Probe Microscopy
- Reports on Progress in Physics
- Reviews in Computational Chemistry
- Reviews of Modern Physics
- Science
- Superconductor Science and Technology
- Surface Science
- Tetrahedron
- Tetrahedron: Asymmetry
- Tetrahedron Letters
Masa Katagiri Home Page | NRIM Home Page | Scientific Links | Fun | Queen's University of Belfast | ASG | library | HENSA Archives | Yahoo! UK & Ireland | CODATA | Yinon Bentor's Periodic Table |

Masa Katagiri katagiri@nrim.go.jp

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Chemistry Software

revised 2003/01/22

Masa Katagiri

Scientific Programs and Links

Constants

Ab Initio Programs

Density Functional Programs

Quantum Molecular Dynamics, Car-Parrinello Methods

Basis Sets

Pseudopotentials

Crystallography Programs

Desktop Publishing and Molecular Modeling

Useful Programs for Molecular Dynamics

Modeling

Molecular Dynamics and Mechanics Programs

Nomenclature

NMR Processing and Prediction

Molecular and Scientific Visualization

Polymer

Poisson-Boltzmann quation

Potential Functions and Databases

Semiempirical Programs

Tight Binding

Misc. Programs

Data Analysis and Conversion Programs

Other Links for Scientific Programs

Useful subroutines

Databases

Protein Databank

Periodic Tebles

Reference Search

Integrated Graphics Systems

Academic Societies

Molecular Simulations, Inc.

Home Pages

Home Pages - Universities etc.

Academic Societies

Publishers & Book Shops

ARTICLES ONLINE

Journals

Chemistry Software