Theoretical Chemistry

program packages, software libraries, etc.

theoretical chemistry

(see also: molecular modelling)

• QCPE, quantum chemistry program exchange (just a single home page; further contacts possible only via telnet/ftp); more information: QCPE via CCL
• CCP5 program library for MD and related things, including ftp-access to the programs from Allen&Tildesley’s book: “Computer Simulation of Liquids”
• Computer Physics Communications and its program library
• MOLSCAT program for inelastic scattering, by J.M.Hutson and S.Green (click here to access a local copy of the documentation)
• Mopac7, a free mopac version
• Spartan, by Wavefunction Inc. (Warren Hehre, UC Irvine)
• Jaguar, by Schroedinger Inc.
• PC-GAMESS, the port of GAMESS-US to Windows-PC’s and linux PC’s(!) (see also thismirror site for a possibly faster connection)
• GAMESS-UK, by Computing for Science Ltd.
• Gamess-US, and the corresponding e-mail discussion list
• annotated inputs and outputs of Gamess, by Brian Salter Duke
• Dalton, another free quantum chemistry code
• the official Molpro homepage in Cardiff (this is the official mirror in Stuttgart).
• the official Gaussian homepage, now including an online manual (aka TechInfo) for G98
• Turbomole, by Ahlrichs et al., Karlsruhe; since Oct 2005 distributed by COSMOlogic, now with online manual and a good(!) tutorial
• ORCA, by Frank Neese (Univ Bonn)
• Q-Chem, by Head-Gordon, Gill, et al.
• AcesII
• ADF
• CRYSTAL03 in Torino (old link, including some Crystal98 stuff) (and in Daresbury), online tutorial
• PWscf, a free plane-wave SCF code from SISSA, Trieste
• FLEUR, the official FLAPW implementation
• WIEN2k, another FLAPW implementation
• Siesta, another alternative for solid state DFT calculations
• VASP, a CPMD competitor from the University of Vienna
• PHONON, for calculation of solid state phonons, with interfaces to VASP, Siesta, Wien2k,… (oops: only for Windows!)
• Babel: molecular modeling file format conversion, and its successor Open Babel
• MOLGEN, by the Department of Mathematics II, University of Bayreuth
• Mike Allen’s personal home page, with a link to all the demonstration program source codes of the book “Computer Simulation of Liquids” by Allen/Tildesley
• genamics.com software: lists of links to free software for molecular biology and biochemistry (including linux as platform)
• Rolf Claessen’s list of chemistry software
• MOPAC manual (older version)
• AIMPAC, a program suite for Bader’s Atoms in Molecules
• NAMD, an MD code for large-scale biomolecular simulations, by the Theoretical Biophysics Group at the University of Illinois
• Lucretius MD code by G.D.Smith (Utah)
• CHARMM
• DYNAMO library for molecular dynamics, including QM/MM options, by M.J.Field et al.
• NWChem, the CompChem software from EMSL, Pacific Northwest National Lab (not fully up to molpro standards on the ab initio side, but can do lots of dynamics, e.g. QM/MM, CP(!), force fields, etc., and is geared towards workstation clusters and parallel computing)
• WebMO, a WWW-interface to Gaussian, GAMESS and MOPAC
• TINKER, free MD package by Jay Ponder et al., Washington University, St. Louis
• Moldy, free MD package by Keith Refson, Oxford (including a list of other free and commercial MD codes)
• GROMACS, possibly the best free MD package out there…
• AMBER
• chemistry software for linux by Nikodem Kuznik (actually part of the chemistry section of the WWW virtual library)
• chemistry software for linux by Carlo Nervi
• Structural biology software database by the Klaus Schulten group
• AMMP MD and modeling program, containing a modified version of the UFF force field
• AMBER parameter database by Richard Bryce, U Manchester
• computational biochemistry resources, appendix of a book Computational Biochemistry and Biophysics, giving many links to MD programs, force fields, protein folding, etc. (see also this indirect link)
• CPMD program home page (free license, download, FAQ, etc.)
• MACSIMUS, a free force field and MD software for macromolecules, proteins, etc.
• Avisto, an integrative CompChem environment by Astonis
• LAMMPS molecular dynamics by Sandia National Lab, a massively parallel C++ package containing lots of goodies (tons of standard force fields, rigid body, coarse grained, reaxFF, rrespa, etc.)
• Pizza.py toolkit for MD trajectory postprocessing.
• nanoHUB, live online simulations and program exchange for nano simulations of all kinds

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global optimization, docking, folding, …

• Adaptive Simulated Annealing by Lester Ingber (click here for old link)
• Genetic Algorithm in FORTRAN by David L.Carroll
• Parallel Genetic Algorithm Library, by David Levine,
• Molecular Packing Analysis Software, by D.E.Williams (Louisville)
• Computational Biology Tools by the Cornell Theory Center (Elber & Scheraga), including e.g. protein folding by molecular dynamics with minimization, but also molecular dynamics, protein recognition, etc.
• AutoDock, by Art Olson’s group at the Scripps Research Institute
• Molecular Modelling Toolkit, by Konrad Hinsen
• Multidock, for protein-protein docking
• NMRCLUST, automatic clustering of an ensemble of protein structures
• Structural biology software database by the Klaus Schulten group
• Polymorph Predictor (crystal structure prediction, by Accelrys (ex-MSI)
• UPACK (crystal structure prediction, by B.P.van Eijck, Utrecht)
• FlexX, molecular docking by Tripos
• DSSP secondary structure assignment standard program by Kabsch and Sander
• CaGe, a generator of graphs, plus translation into 3D coordinates
• deap, distributed evolutionary algorithms in python

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molecular viewers/manipulators

• RasMol
• enhanced RasMol, by UC Berkeley
• Molden (here is a brief description of the two main control windows)
• Jmol, an OpenScience/open source molecule viewer and editor
• Marvin, a Java program for drawing/displaying chemical structures on the web
• gOpenMol by Leif Laaksonen, part of the OpenMol project by Geerd Diercksen (Garching) (gOpenMol now also comes with a tutorial)
• Spock, a molecular graphics program by Jon A. Christopher (runs also under Linux!)
• VMD, visual molecular dynamics, by Klaus Schulten’s Theoretical Biophysics Group at the University of Illinois (also responsible for the NAMD molecular dynamics code)
• Molekel by Stefan Portmann, Swiss Center for Scientific Computing
• Structural biology software database by the Klaus Schulten group
• PyMOL (see also this link)
• Chemtool, a molecular graphics program for linux (see also this older link)
• WhatIf, a protein structure viewer, analysis, and manipulation program with many useful features (see also this link for a web interface to some features)
• XCrysDen, a solid state and molecules visualization program, with interfaces to Gaussian, Crystal, PWscf, Wien2k,…
• XMakeMol by Matt Hodges
• Ghemical, semiempirical CompChem package with a molecule builder
• Ghemical-GMS, a special Ghemical version as front- and back-end for Gamess
• Gabedit (reads molecule data and molpro/Gaussian output; can produce povray input files)
• Mol2Mol, visual conversion between various molecule file formats, with PoVRay output (sorry, only windows)
• Dino3D, visualization of biomolecules, surfaces, etc. (these pages also include a nice intro to povray)
• UCSF Chimera molecular viewer
• PoVRay raytracer

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general scientific computing

(see also: mathematics)

• Netlib Repository at UTK/ORNL: LAPACK with on-line Users’ Guide 2.0, and similar highly useful libraries (see also the netlib mirror sites in Germany, England, and Norway; unfortunately, they do not carry the LAPACK Users’ Guide);
  see also the new GUI to Lapack
• GAMS : Guide to Available Mathematical Software by the National Institute of Standards and Technology; also including TOMS: Transactions on Mathematical Software (alternative adress) and the NIST Sparse BLAS
• Plato, a modern version of GAMS, aiming at free software for optimization problems
• Numerical Recipes, including full text and downloading of routines (*NOT* free!)
• Numerical Recipes with full text and routine downloading (*NOT* free!), by The Universal Library at Carnegie Mellon
• IMSL
• NAG
• PORT mathematical subroutine library by the Bell Labs (see also this link for yet more software distributed similarly)
• Harwell Software Library, now freely available for academic use
• SciTech software
• UG: adaptive multigrid solution of partial differential equations
• Mathematics Archives, a long list of links to sites with mathematical software
• Matrix Market, a collection of test matrices
• The Fortran Market (old link), with pointers to everything connected with Fortran; see alsoThe Fortran Library
• cfortran, tools for a machine-independent interface between C and Fortran
• freely available software for linear algebra on the web, compiled by Jack Dongarra
• software porting and archive centre for HP-UX
• software porting and archive centre for HP-UX, mirror site of the previous entry in Karlsruhe, provided by the Akademische Software Kooperation
• Akademische Software Kooperation ASK, providing commercial software and licenses at low academic prices
• ASKnet am Rechenzentrum der Uni Stuttgart
• Subroutine On Demand-service for sparse matrices, University Leiden.
• Pseudopack, a pseudo-spectral differentiation software package.
• a fast FFT library by M.Frigo and S.G.Johnson, MIT; but better see the successor:
• FFTW, the “fastest Fourier transform in the west”, by M.Frigo and S.G.Johnson, MIT; impressive performance over a wide variety of machines
• mathematical and graphical libraries at NCAR/UCAR
• mathtools.net, with a collection of links for Fortran programming
• The Scientific Web, offers an overview over “all” known software in science
• the official GNU site
• GNU info tree at the University of Utah
• GNU software index
• OpenScience, a (hopefully growing) collection of (links to) free, open-source programs for all fields of science
• Linux software for scientists, a list by S.Baum
• linux science software list at SuSE
• gnuplot FAQ at Uni Karlsruhe
• Chemistry Software and Information Resources
• Simtel.Net: distribution of shareware, freeware and public domain programs for DOS and Windows (see also alternate U.S. location, and mirror in Germany), also including many other interesting links, e.g. to ports of GNU software to MS-DOS
• ports of gnu utilities to windows by Karl Syring
• tucows, the ultimate collection of winsock software (includes a long list of mirror sites worldwide, see e.g.: mirror site in Germany)
• the official GNU homepage
• Scientific Software for Linux
• Essential Lahey Fortran 90, a proper subset of the full Fortran 90 specification, eliminating most of the old Fortran 77 junk (stand-alone compiler for free(!), full system at $79)
• SAL (Scientific Applications on Linux), a collection of information and links to scientific software on linux boxes, e.g. BLAS optimized for single Pentium Pro/Pentium II processors (see also the German mirror)
• Intel Pentium linux libraries (BLAS, FFT, Performance Monitoring, Extended Precision), by the Sandia National Lab (Greg Henry)
• ATLAS, automatically tuned linear algebra software by Whaley and Dongarra, i.e. produce your own machine-tuned BLAS! (now at this link)
• ITXGEMM, a PentiumIII-tuned DGEMM implementation
• Linux International
• Linuxberg (FH-Heilbronn mirror): tons of linux software for all purposes…
• PhatLinux: Linux installed in and running from a Windows partition (oops, I would want it the other way around…)
• VMware: running Windows programs on a “virtual machine” from within linux (or, actually and more generally, VMware can run multiple virtual computers on a single PC at the same time, in particular also linux within windows, etc.)
• Wine, a free implementation of Windows on unix; allows unmodified Windows 3.1/96/NT binaries to run under Intel unixes, including Linux, FreeBSD, and Solaris.
• Jaz/Zip drive maintenance program for linux
• The Linux Documentation Project
• MPI and MPICH pages of the Mathematics and Computer Science Division of the Argonne National Laboratory
• High performance computing linux vom Institut für Techno- und Wirtschaftsmathematikdistribution der Uni Kaiserslautern, enthält u.a. MPI/MPICH in Verbindung mit Portland Fortran und C und einige Visualisierungstools
• Mersenne Twister, a superior random number generator by M.Matsumoto and T.Nishimura
• PGPLOT, simple drawings directly from Fortran
• DISLIN, a free graphics library for f90/f95 (and other languages)
• gnuplotfortran, a way to control a gnuplot session from within an f90/f95 program
• DDD, a graphical frontend debugger, designed to provide a good GUI for several line debuggers like dbx, xdb, etc.
• Intel Fortran compiler for Linux
• Intel Linux Fortran Compiler Comparisons by Polyhedron Software
• Grace homepage (WYSIWYG plotting for X Windows; included in SuSE linux as “xmgrace”)
• PC Cluster Consortium, with their Score PC cluster software
• Clusters@top500.org, another site with lots of cluster software, and also hardware performance rankings etc.
• Linux on laptops, BIG selection of links and HowTo’s
• Putty, a free Windows ssh/scp client
• Unix with mobile computers, another linux on laptops site, including the linux laptop mailing list

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typesetting and text processing

• DANTE, Deutschsprachige Anwendervereinigung TeX, with link to the comprehensive TeX Archive Network CTAN and other helpful links…
• TeX Users Group, with links to all of the above, plus a lot of other useful stuff, including acollection of TeX-related mailing lists
• TeX2gif, conversion of LaTeX to gif (e.g. for displaying LaTeX equations in MS-Word or on web pages)

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Last updated on Wed Jan 09 08:45:54 MET DST 2013