Molecular Dynamics Software
A comprehensive list of molecular dynamics simulation software
Molecular Dynamics (MD) simulations are a cornerstone of computational chemistry, biophysics, and materials science, enabling researchers to study the physical movements of atoms and molecules over time. Choosing the right MD software is crucial for achieving reliable and efficient simulation results. This guide provides a detailed overview of various MD software tools, highlighting their capabilities, computational efficiency, and application scopes. Whether you are a seasoned researcher or a student just beginning in the field, understanding the different options available can help you select the software that best fits your project's needs.
The following table summarizes the key features of popular MD software tools, including
- Name: The official name of the software, linked to its homepage where more detailed information can be accessed.
- Force Field: The types of force fields supported by the software. Force fields are mathematical models used to calculate the forces between atoms in molecular simulations. Different force fields are tailored for different types of molecules such as proteins, nucleic acids, or organic molecules.
- Type of Simulation: Describes the kinds of molecular simulations the software is capable of performing. This includes classical molecular dynamics, quantum mechanics/molecular mechanics hybrid simulations (QM-MM), and other specialized types of molecular simulations.
- HPC Capability: Indicates the software's ability to perform efficiently on High-Performance Computing systems. This includes support for parallel computing, which is critical for running large-scale simulations efficiently.
- GPU: Indicates whether the software supports GPU (Graphics Processing Unit) acceleration. GPU acceleration can significantly speed up molecular dynamics simulations by performing parallel computations faster than a standard CPU.
- Customizable: Reflects whether the software can be customized or extended through scripting, plugins, or source code modification. Customizability is important for researchers who need to implement specialized simulation conditions or analysis workflows.
- License: Describes the licensing model under which the software is distributed. This can range from proprietary to free open source. Some software might be available under multiple licensing terms depending on the use case (e.g., academic vs. commercial use).
This information is intended to aid in making an informed decision about which software to utilize for your molecular dynamics simulations.
| Name | Force Field | Type of Simulation | HPC Capability | GPU | Customizable | License |
|---|---|---|---|---|---|---|
AMBER | Classical MD | High Performance | Yes | Yes | Proprietary, Free open source | |
Various (customizable) | Classical MD, Biomolecular simulations | High Performance | Yes | Yes | Proprietary, gratis, commercial | |
ReaxFF, UFF, QM-MM | QM, DFT, semi-empirical | High Performance | Yes | Yes | Proprietary, commercial, gratis trial | |
Customizable | Classical MD, QM-MM | High Performance | Yes | Yes | Mixed: free open source (GNU GPL) & commercial | |
Various (plugin-based) | Molecule building, Editing | Medium | No | Yes | Free open source GNU GPL | |
OPLS | Classical MD | Medium | No | Limited | Proprietary | |
CHARMM | Classical MD | High Performance | Yes | Yes | Proprietary, commercial | |
N/A | Chemical kinetics | Low | No | No | Proprietary | |
Various | Classical MD, QM, QM-MM | High Performance | Yes | Yes | Free open source GNU GPLv2 or later | |
Various | Classical MD | High Performance | Yes | Yes | Proprietary, commercial or gratis | |
Various | Small molecule, Protein-ligand docking | High Performance | Yes | Yes | Proprietary, trial available | |
Customizable | Protein folding | Medium | No | Limited | Proprietary, commercial or gratis | |
Customizable | Protein design | Low | No | No | Proprietary, commercial or gratis | |
GROMOS, OPLS, AMBER | Classical MD | High Performance | Yes | Yes | Free open source GNU GPL | |
GROMOS | Classical MD | High Performance | Yes | Limited | Proprietary, commercial | |
Various | Classical MD, Coarse-grained MD | High Performance | Yes | Yes | Free open source, GNU GPLv2 | |
OPLS-AA, MMFF | Classical MD | High Performance | No | Limited | Proprietary | |
Various | Classical MD, QM | High Performance | Yes | Yes | Proprietary, trial available | |
Various | Classical MD, QM | High Performance | Yes | Yes | Proprietary, trial available | |
CHARMM, Custom | Classical MD | Medium | Yes | Yes | Proprietary, free trial available | |
Various | Classical MD | High Performance | No | Yes | Free open source GNU GPL | |
Various | Classical MD | High Performance | No | Limited | Proprietary | |
Various | Fluid simulations | High Performance | No | Yes | Free open source | |
AMBER, CHARMM | Classical MD | High Performance | Yes | Yes | Free open source MIT | |
CHARMM, AMBER | Classical MD | High Performance | Yes | Yes | Proprietary, free academic use | |
Various | QM, MD, QM-MM | High Performance | No | Yes | Free open source, Educational Community License version 2.0 | |
Custom | Protein optimizing | Medium | No | Yes | Proprietary | |
Custom | Free energy calculations | Medium | No | Yes | Free open source GNU GPLv2 or later | |
Various | QM, semi-empirical | High Performance | No | Yes | ||
Various | Computational nanoscience | High Performance | No | Yes | Proprietary, gratis | |
Various | MM, DFT, semiempirical | High Performance | No | Yes | Proprietary | |
Various | MM, QM | Medium | No | Limited | Proprietary, free trial available | |
Various | QM, ab initio MD | High Performance | Yes | Yes | Proprietary, trial licenses available | |
Various | Classical MD, QM-MM | High Performance | Yes | Yes | Proprietary, gratis | |
Various | Molecular graphics, modeling | High Performance | No | Yes | Proprietary, free academic use | |
Various | Molecular graphics, modeling | High Performance | Yes | Yes | Proprietary |
Run molecular dynamics simulation software online
With the increasing demand for flexible and scalable computational resources, running molecular dynamics (MD) simulations online has become an essential capability for researchers across disciplines. DiPhyx is designed to meet this need by offering a cloud-native platform where you can run a wide range of MD simulation software directly from your browser, without the need to manage complex installations or dedicated hardware.
Key Benefits of Running MD simulation software on DiPhyx:
- Scalability: DiPhyx allows you to harness the power of high-performance computing (HPC) clusters and cloud resources, scaling your simulations from small to large systems with ease. Whether you're running a short test or a long-term study, DiPhyx ensures that you have the computational power you need, when you need it.
- Ease of Use: The DiPhyx platform offers an intuitive interface that makes it simple to set up, run, and monitor your MD simulations. With pre-configured environments for popular MD software, you can start simulations with just a few clicks, eliminating the hassle of software installation and configuration.
- Access from Anywhere: As a fully online platform, DiPhyx provides the flexibility to run your MD simulations from any location, on any device. This means you can conduct your research remotely, collaborate with team members in different parts of the world, and keep your projects moving forward without interruption.
- Automatic Updates: Running your simulations on DiPhyx ensures that you always have access to the latest versions of your preferred MD software. The platform is regularly updated with the latest features and performance enhancements, so you can focus on your research without worrying about software maintenance.
- Data Management and Security: DiPhyx not only simplifies the execution of MD simulations but also offers robust data management features. Your simulation data is securely stored in the cloud, with options for easy sharing, collaboration, and compliance with regulatory standards.
Available Molecular Dynamics Software to Run Online on DiPhyx
DiPhyx now supports several powerful molecular dynamics (MD) software packages, enabling researchers to conduct simulations with ease and efficiency. These tools are fully integrated into the platform, allowing you to take advantage of DiPhyx's scalable computing resources and user-friendly interface.
- AMBERMD: AMBER (Assisted Model Building with Energy Refinement) is a widely used MD software suite designed for simulating biomolecules. Known for its accuracy and efficiency, AMBERMD supports a variety of force fields and simulation types, making it ideal for studying the dynamics of proteins, nucleic acids, and other complex biological systems.
- GROMACS: GROMACS (GROningen MAchine for Chemical Simulations) is a high-performance MD package primarily designed for simulating proteins, lipids, and nucleic acids. Renowned for its speed and flexibility, GROMACS supports a wide range of simulations, from small molecules to large biomolecular systems, and offers advanced features like replica exchange and hybrid quantum mechanics/molecular mechanics (QM/MM) simulations.
- LAMMPS: LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a versatile MD simulator that excels in modeling materials science problems, including solid-state systems, soft matter, and coarse-grained biomolecular simulations. Its modular structure allows users to customize simulations with a variety of force fields and integration methods, making it a popular choice for both academic and industrial research.
These software packages are now available on DiPhyx, giving you access to robust MD simulation tools in a cloud-native environment. Simply select the software that best suits your research needs and start running simulations with the power and flexibility of DiPhyx.
Note
We are progressively adding more MD software tools to the DiPhyx platform. If you need us to prioritize the integration of specific software, please send us an email at info@diphyx.com. We value your input and look forward to enhancing your experience with DiPhyx.
DiPhyx is your gateway to running advanced molecular dynamics simulations online, offering the computational power and convenience you need to accelerate your scientific discoveries.