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Software

R Di Felice, M Mayes, R Richard, D Williams-Young, G Chan, W de Jong, N Govind, M Head-Gordon, M Hermes, K Kowalski, X Li, H Lischka, K Mueller, E Mutlu, A Niklasson, M Pederson, B Peng, R Shepard, E Valeev, M van Schilfgaarde, B Vlaisavljevich, T Windus, S Xantheas, X Zhang, P Zimmerman, A Perspective on Sustainable Computational Chemistry Software Development and Integration, JCTC 19, 7056 (2023) – doi

S Lehtola, A Karttunen, Free and open source software for computational chemistry education, WCMS 12, e1610 (2022)


A Thompson, H Aktulga, R Berger, D Bolintineanu, W Brown, P Crozier, P in 't Veld, A Kohlmeyer, S Moore, T Nguyen, R Shan, M Stevens, J Tranchida, C Trott, S Plimpton, LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales, CPC 271, 108171 (2022) – doi, LAMMPS

B Hourahine, B Aradi, V Blum, F Bonafe, A Buccheri, C Camacho, C Cevallos, M Deshaye, T Dumitrica, A Dominguez, S Ehlert, M Elstner, T van der Heide, J Hermann, S Irle, J Kranz, C Kohler, T Kowalczyk, T Kubar, I Lee, V Lutsker, R Maurer, S Min, I Mitchell, C Negre, T Niehaus, A Niklasson, A Page, A Pecchia, G Penazzi, M Persson, J Rezac, C Sanchez, M Sternberg, M Stohr, F Stuckenberg, A Tkatchenko, V Yu, T Frauenheim, DFTB+, a software package for efficient approximate density functional theory based atomistic simulations, JCP 152, 124101 (2020) – doi, DFTB+

M Abraham, T Murtola, R Schulz, S Pall, J Smith, B Hess, E Lindahl, GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers, SoftwareX 1, 19 (2015) – doi, GROMACS

G Kresse, J Furthmuller, Efficient Iterative Schemes for Ab Initio Total-Energy Calculations Using a Plane-Wave Basis Set, PRB 54, 11169 (1996) – doi, VASP


M J Frisch etal, Gaussian 16, Revision C.01 (Gaussian Inc, Wallingford CT, 2016) – Gaussian

Visualizers (free)

Avogadro

Jmol

MacMolPlt

MOLDEN

Molekel

VMD

XCrySDen

Molecular modeling environments

With solvers

ADF

ChemShell

HyperChem (molecules only)

Materials Studio by Accelrys

MedeA

MStudio Mindlab

Schrodinger (Jaguar, Maestro, Macromodel)

Spartan (molecules only)

Without solvers

Atomistix ToolKit (academic)

ChemCraft

Gabedit (free)

PyADF

Pyiron (IDE for computational materials science)

WebMO (free online version requiring Perl and Apache server)

Other environments

Rosetta (academic, proteins and nucleic acids)

Solvers

Wikipedia

Ab initio molecules and crystals

BigDFT (free, wavelets)

CP2K (free, GTO and PW +MD +TB +classical MD)

CRYSTAL (GTO)

FHI-aims (numerical AO)

Gaussian (GTO)

NWChem (academic)

Octopus (grid-based +TDDFT)

Ab initio molecules

Columbus (academic, MRCI)

Firefly (academic)

FreeON (free, linear scaling +PBC +MD)

GAMESS (academic)

MOLCAS

Molpro (MRCI)

ORCA (forum)

Q-Chem

TeraChem

Turbomole

Ab initio crystals

ABINIT (free)

CASTEP (+MD)

Conquest (academic, linear scaling)

GPAW (grid-based projector-augmented wave method)

ONETEP (Wannier, linear scaling)

Quantum ESPRESSO (free)

SIESTA (academic, optimized LCAO, linear scaling + MD)

VASP (+MD)

WIEN2k (augmented PW and local orbitals)

Yambo (free, post-DFT)

Semiempirical

AMPAC (+GUI)

MOPAC (academic)

Density functional tight binding

DFTB+ (academic +DFT)

xtb (academic)

Tight binding

Fireball

NEMO-3D (free)

Plato (academic +DFT)

Classical molecular mechanics

AMBER (biomolecules)

CHARMM

CONFLEX

GROMACS (free)

GULP (academic)

LAMMPS (free)

NAMD (free)

TINKER (free)

Other solvers

BerkeleyGW (academic)

ELSI - ELectronic Structure Infrastructure

Other simulators and solvers

ADC-connect - algebraic-diagrammatic construction (python)

ANT - nonadiabatic MD (academic)

CASINO - quantum MC (academic)

Dirac - relativistic effects (academic)

libAtoms+QUIP - MD+TB

MCTDH - quantum MD (academic)

MS2 - MD for thermodynamics of liquids

MultiPsi - MCSCF (python)

NEXMD - nonadiabatic MD (free)

PYXAID - nonadiabatic MD (free)

QMCPACK - quantum MC (free)

QWalk - quantum MC (free)

TurboRVB - quantum MC (free)

Materials modeling environments

AiiDA - Automated Interactive Infrastructure and Database for Computational Science

Atomate

ASE - Atomic Simulation Environment

ESL - Electronic Structure Library (CECAM)

JARVIS - Joint Automated Repository for Various Integrated Simulations (NIST)

MatCloud - based on VASP

Pymatgen - Python Materials Genomics

Multiscale modeling

DAMASK - the Dusseldorf Advanced Material Simulation Kit

Computational geometry

CAT - Compound Attachment Tool

LEADOMISE - workflow for directed medicinal chemistry design

TRAVIS - Trajectory Analyzer and Visualizer

Symmetry

MolSym - Python package for handling molecular symmetry

QSym2 - Quantum Symbolic Symmetry Analysis Program for Electronic Structure

SeeK-path - k-path finder and visualizer

Other tools

ATAT - Alloy Theoretic Automated Toolkit

CREST - Conformer-Rotamer Ensemble Sampling Tool

FDA - Computation of Atomic Orbitals (free, Density Functional method and the Xalpha functional)

LocVib - vibrations localization

Molecular Dynamics Studio - simplifies MD in LAMMPS

MOVIPAC - vibrational spectroscopy (numerical derivatives)

Multiwfn - Multifunctional Wavefunction Analyzer

NBO6 - Natural Bond Orbital analysis (see also NBO5)

OpenMM - MD Toolkit (free)