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	AMBER	Classical MD	High Performance	Yes	Yes	Proprietary, Free open source
Abalone	Various (customizable)	Classical MD, Biomolecular simulations	High Performance	Yes	Yes	Proprietary, gratis, commercial
ADF	ReaxFF, UFF, QM-MM	QM, DFT, semi-empirical	High Performance	Yes	Yes	Proprietary, commercial, gratis trial
Ascalaph Designer	Customizable	Classical MD, QM-MM	High Performance	Yes	Yes	Mixed: free open source (GNU GPL) & commercial
Avogadro	Various (plugin-based)	Molecule building, Editing	Medium	No	Yes	Free open source GNU GPL
BOSS	OPLS	Classical MD	Medium	No	Limited	Proprietary
CHARMM	CHARMM	Classical MD	High Performance	Yes	Yes	Proprietary, commercial
CHEMKIN	N/A	Chemical kinetics	Low	No	No	Proprietary
CP2K	Various	Classical MD, QM, QM-MM	High Performance	Yes	Yes	Free open source GNU GPLv2 or later
Desmond	Various	Classical MD	High Performance	Yes	Yes	Proprietary, commercial or gratis
Discovery Studio	Various	Small molecule, Protein-ligand docking	High Performance	Yes	Yes	Proprietary, trial available
fold.it	Customizable	Protein folding	Medium	No	Limited	Proprietary, commercial or gratis
FoldX	Customizable	Protein design	Low	No	No	Proprietary, commercial or gratis
GROMACS Github	GROMOS, OPLS, AMBER	Classical MD	High Performance	Yes	Yes	Free open source GNU GPL
GROMOS	GROMOS	Classical MD	High Performance	Yes	Limited	Proprietary, commercial
LAMMPS Github	Various	Classical MD, Coarse-grained MD	High Performance	Yes	Yes	Free open source, GNU GPLv2
MacroModel	OPLS-AA, MMFF	Classical MD	High Performance	No	Limited	Proprietary
MAPS	Various	Classical MD, QM	High Performance	Yes	Yes	Proprietary, trial available
Materials Studio	Various	Classical MD, QM	High Performance	Yes	Yes	Proprietary, trial available
MBN Explorer	CHARMM, Custom	Classical MD	Medium	Yes	Yes	Proprietary, free trial available
MDynaMix	Various	Classical MD	High Performance	No	Yes	Free open source GNU GPL
MOE	Various	Classical MD	High Performance	No	Limited	Proprietary
ms2	Various	Fluid simulations	High Performance	No	Yes	Free open source
OpenMM Github	AMBER, CHARMM	Classical MD	High Performance	Yes	Yes	Free open source MIT
NAMD	CHARMM, AMBER	Classical MD	High Performance	Yes	Yes	Proprietary, free academic use
NWChem	Various	QM, MD, QM-MM	High Performance	No	Yes	Free open source, Educational Community License version 2.0
Protein Local Optimization Program	Custom	Protein optimizing	Medium	No	Yes	Proprietary
Q	Custom	Free energy calculations	Medium	No	Yes	Free open source GNU GPLv2 or later
QuantumATK	Various	QM, semi-empirical	High Performance	No	Yes
SAMSON	Various	Computational nanoscience	High Performance	No	Yes	Proprietary, gratis
Scigress	Various	MM, DFT, semiempirical	High Performance	No	Yes	Proprietary
Spartan	Various	MM, QM	Medium	No	Limited	Proprietary, free trial available
TeraChem	Various	QM, ab initio MD	High Performance	Yes	Yes	Proprietary, trial licenses available
TINKER	Various	Classical MD, QM-MM	High Performance	Yes	Yes	Proprietary, gratis
UCSF Chimera	Various	Molecular graphics, modeling	High Performance	No	Yes	Proprietary, free academic use
YASARA	Various	Molecular graphics, modeling	High Performance	Yes	Yes	Proprietary

We are progressively adding these software 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.