Molecular Dynamics Engines

• AMBER: suite of biomolecular simulation programs (standalone)

  

• CHARMM: Chemistry at HARvard Macromolecular Mechanics (standalone)

  

• CHARMM-GUI:

  

• GENESIS: GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models
  

  

• 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: High-Throughput Molecular Dynamics for Molecular Discovery
  

  

• 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.

• 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
  

• QwikMD: QwikMD — Integrative Molecular Dynamics Toolkit for Novices and Experts

  

• 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: STORMM: Structure and TOpology Replica Molecular Mechanics for chemical simulations

  

• 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)
  

• openff-toolkit:
  

  

• openmmtools: Time Step Rescaling Recovers Continuous-Time Dynamical Properties for Discrete-Time Langevin Integration of Nonequilibrium Systems
  

  

Interoperable

• SIRE: An interoperability engine for prototyping algorithms and exchanging information between molecular simulation programs

  

ML-enabled

• DeepDriveMD: Deep-Learning Driven Adaptive Molecular Simulations (standalone)
  

• MLCGMD: Simulate Time-integrated Coarse-grained Molecular Dynamics with Multi-scale Graph Networks
  

  

• Medbi et al.: Enhanced Sampling with Machine Learning

  

• NeuralMD: A Multi-Grained Symmetric Differential Equation Model for Learning Protein-Ligand Binding Dynamics
  

  

• torchmd: TorchMD: A Deep Learning Framework for Molecular Simulations
  

  

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.