AMBER: suite of biomolecular simulation programs (standalone)
CHARMM: Chemistry at HARvard Macromolecular Mechanics (standalone)
CHARMM-GUI:
GaMD: Gaussian Accelerated Molecular Dynamics (GaMD) is a biomolecular enhanced sampling method that works by adding a harmonic boost potential to smoothen the system potential energy surface.
Gromacs: GROMACS is a versatile package for performing molecular dynamics simulations, primarily designed for simulations of proteins, lipids, and nucleic acids.
HTMD:
HTMD: a molecular-specific programmable environment to prepare, handle, simulate, visualize and analyze molecular systems (standalone)
LAMMPS: Molecular Dynamics Simulator and much more
NAMD: NAMD is a parallel molecular dynamics code for high-performance simulation of large biomolecular systems, recognized for its scalability and efficiency.
openff-toolkit:
OpenMM: OpenMM is a high-performance toolkit for molecular simulation, offering extensive language bindings and a flexible platform for developing high-performance algorithms.
OpenMMDL: Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes
openmmtools:
QwikMD:
SENPAI: SENPAI is a molecular dynamics simulation software aimed at students and academia, designed to simulate molecular systems of educational and academic interest efficiently.
STORMM:
Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS (online)
WEBGRO: MD simulation online with GROMACS (online)
YAMACS: graphical user interface for the GROMACS program (standalone)
GENESIS: The GENESIS package contains two MD programs (atdyn and spdyn), trajectory analysis programs, and other useful tools.
GENESIS:
Interoperable
SIRE: An interoperability engine for prototyping algorithms and exchanging information between molecular simulation programs
MLCGMD: Simulate Time-integrated Coarse-grained Molecular Dynamics with Multi-scale Graph Networks
NeuralMD:
torchmd:
Water
PyRod: PyRod is a Python software for generating dynamic molecular interaction fields and pharmacophore features based on the protein environment of water molecules in molecular dynamics simulations. .)