Orac is a molecular dynamics simulation engine for studying complex biomolecular systems at the atomistic level. It is designed particularly for simulations of solvated biomolecules, with methods for investigating molecular motion, conformational changes and free-energy landscapes.
The software combines classical molecular dynamics algorithms with enhanced sampling techniques. Researchers can perform conventional simulations under different thermodynamic conditions or investigate processes that are difficult to sample using ordinary molecular dynamics.
Orac includes methods for replica exchange, metadynamics and non-equilibrium simulations. These approaches are useful for studying molecular transitions, exploring free-energy surfaces and calculating thermodynamic properties.
The simulation engine uses MPI and OpenMP parallel processing to distribute computational work across modern computing systems. It is aimed at researchers requiring detailed control over molecular simulations rather than interactive molecular modelling.
This is free and open source software.
Key Features
- Performs atomistic molecular dynamics simulations of complex biomolecular systems.
- Supports simulations of molecules in explicit solvent environments.
- Offers NVE, NVT and NPT statistical-mechanical ensembles.
- Uses the r-RESPA multiple time-step integration algorithm.
- Supports Smooth Particle Mesh Ewald calculations for long-range electrostatic interactions.
- Provides hybrid Hamiltonian replica exchange methods for enhanced sampling.
- Supports solute tempering and torsional tempering approaches.
- Includes serial generalised ensemble simulation methods.
- Provides well-tempered metadynamics for exploring molecular free-energy landscapes.
- Supports Self-Healing Umbrella Sampling for enhanced exploration of molecular configurations.
- Offers steered molecular dynamics and non-equilibrium driven trajectories.
- Supports free-energy calculations using Jarzynski and Crooks non-equilibrium relations.
- Provides non-equilibrium alchemical transformations for studying molecular free-energy differences.
- Uses MPI parallelism for replica exchange and generalised ensemble simulations.
- Employs OpenMP parallelism for force calculations through particle decomposition.
- Includes example simulations covering thermodynamic ensembles, enhanced sampling and alchemical calculations.
Website: www1.chim.unifi.it/orac
Support:
Developer: Massimo Marchi, Piero Procacci
License: GNU General Public License
Orac is written in Fortran. Learn Fortran with our recommended free books and free tutorials.
Related Software
| Molecular Dynamics and Simulation Tools | |
|---|---|
| GROMACS | High-performance molecular dynamics simulations and analysis |
| LAMMPS | Classical molecular dynamics for materials and particle modelling |
| OpenMM | GPU-accelerated toolkit for custom molecular simulations |
| Orac | Parallel molecular dynamics for solvated biomolecular systems |
| MDynaMix | Molecular dynamics simulations of rigid and flexible mixtures |
| OpenMD | Molecular dynamics engine for complex materials and liquids |
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