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.

NameForce FieldType of SimulationHPC CapabilityGPUCustomizableLicense
AMBERAMBERClassical MDHigh PerformanceYesYesProprietary, Free open source
AbaloneVarious (customizable)Classical MD, Biomolecular simulationsHigh PerformanceYesYesProprietary, gratis, commercial
ADFReaxFF, UFF, QM-MMQM, DFT, semi-empiricalHigh PerformanceYesYesProprietary, commercial, gratis trial
Ascalaph DesignerCustomizableClassical MD, QM-MMHigh PerformanceYesYesMixed: free open source (GNU GPL) & commercial
AvogadroVarious (plugin-based)Molecule building, EditingMediumNoYesFree open source GNU GPL
BOSSOPLSClassical MDMediumNoLimitedProprietary
CHARMMCHARMMClassical MDHigh PerformanceYesYesProprietary, commercial
CHEMKINN/AChemical kineticsLowNoNoProprietary
CP2KVariousClassical MD, QM, QM-MMHigh PerformanceYesYesFree open source GNU GPLv2 or later
DesmondVariousClassical MDHigh PerformanceYesYesProprietary, commercial or gratis
Discovery StudioVariousSmall molecule, Protein-ligand dockingHigh PerformanceYesYesProprietary, trial available
fold.itCustomizableProtein foldingMediumNoLimitedProprietary, commercial or gratis
FoldXCustomizableProtein designLowNoNoProprietary, commercial or gratis
GROMACS GithubGROMOS, OPLS, AMBERClassical MDHigh PerformanceYesYesFree open source GNU GPL
GROMOSGROMOSClassical MDHigh PerformanceYesLimitedProprietary, commercial
LAMMPS GithubVariousClassical MD, Coarse-grained MDHigh PerformanceYesYesFree open source, GNU GPLv2
MacroModelOPLS-AA, MMFFClassical MDHigh PerformanceNoLimitedProprietary
MAPSVariousClassical MD, QMHigh PerformanceYesYesProprietary, trial available
Materials StudioVariousClassical MD, QMHigh PerformanceYesYesProprietary, trial available
MBN ExplorerCHARMM, CustomClassical MDMediumYesYesProprietary, free trial available
MDynaMixVariousClassical MDHigh PerformanceNoYesFree open source GNU GPL
MOEVariousClassical MDHigh PerformanceNoLimitedProprietary
ms2VariousFluid simulationsHigh PerformanceNoYesFree open source
OpenMM GithubAMBER, CHARMMClassical MDHigh PerformanceYesYesFree open source MIT
NAMDCHARMM, AMBERClassical MDHigh PerformanceYesYesProprietary, free academic use
NWChemVariousQM, MD, QM-MMHigh PerformanceNoYesFree open source, Educational Community License version 2.0
Protein Local Optimization ProgramCustomProtein optimizingMediumNoYesProprietary
QCustomFree energy calculationsMediumNoYesFree open source GNU GPLv2 or later
QuantumATKVariousQM, semi-empiricalHigh PerformanceNoYes
SAMSONVariousComputational nanoscienceHigh PerformanceNoYesProprietary, gratis
ScigressVariousMM, DFT, semiempiricalHigh PerformanceNoYesProprietary
SpartanVariousMM, QMMediumNoLimitedProprietary, free trial available
TeraChemVariousQM, ab initio MDHigh PerformanceYesYesProprietary, trial licenses available
TINKERVariousClassical MD, QM-MMHigh PerformanceYesYesProprietary, gratis
UCSF ChimeraVariousMolecular graphics, modelingHigh PerformanceNoYesProprietary, free academic use
YASARAVariousMolecular graphics, modelingHigh PerformanceYesYesProprietary

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 We value your input and look forward to enhancing your experience with DiPhyx.

Contact us
+1 (619) 693-6161
Follow us on
@2023-2024 DiPhyx, Inc.