Molecular_dynamics - Wikiparency

# Molecular dynamics ## Microsim (three.js) <div class="microsim-player">  <p class="wt-pending"><strong>Microsim staged, not yet on the CDN.</strong> <code>Molecular_dynamics.html</code> is built and deploy-ready in <code>Microsims for Dissemination/</code>, but the Netlify project still serves the geometry+spintronics set only. The player is disabled until the deploy lands; the explanatory text below is unchanged.</p>   </div> *Part of the REACTION chemistry hub: molecular dynamics turns the abstract bookkeeping of Enthalpy and Gibbs free energy into visible motion, revealing how the same interatomic forces that build a [[Crystal_structure]] or tangle a Polymer chemistry chain play out through Newton's laws.* > Molecular dynamics (MD) follows a box of atoms one tiny time-step at a time, computing the force on every particle from its neighbours and nudging each forward with Newton's second law. Repeat the loop millions of times and a lifelike movie of matter appears — atoms rattling, clustering, flowing, or freezing. This microsim runs exactly that loop for a Lennard-Jones fluid, letting you set how many particles share the box, how tightly they pack, how hot they are, and how strongly they attract. Turn the dials and watch a gas condense into droplets or a liquid lock into ordered clusters. ## About this microsim The canvas shows a swarm of Lennard-Jones particles evolving under Newton's equations in reduced units. Drag **Particles N** (10–150) to populate the box, then raise **density ρ** (0.05–0.60) to squeeze them together — sparse settings drift like a gas, dense ones jostle like a liquid. Cooling with **target temperature T₀** (0.05–3.00) slows the jitter until clusters and ordered patches nucleate; reheating melts them again. **Interaction strength ε** (0.20–3.00) deepens the attractive well, so at a fixed T₀ a larger ε makes the fluid cohere and condense while a small ε keeps it gaseous. **Simulation speed** (1–8) sets how many integration steps run per frame, trading smoothness for time-to-equilibrium. Structure appears before any equation is quoted — you feel the phase diagram before you read it. ## Related microsims - [[Crystal_structure]] — the ordered lattices that emerge when an MD fluid freezes - Enthalpy — the heat content whose changes track condensation and melting here - Gibbs free energy — the quantity whose minimisation decides which phase you observe - Nanomaterials — a leading application domain for atomistic MD - Polymer chemistry — long-chain systems routinely studied with the same integrator - Ionic bond — a stronger interaction that replaces the LJ well in salts and ceramics - Crystallographic defect — related REACTION microsim - Enriched uranium — related REACTION microsim - Thermal neutron — related REACTION microsim ## Links (Wikipedia order)  `Ab_initio` · `Ab_initio_quantum_chemistry_methods` · `Abalone_(molecular_mechanics)` · `Actinide_chemistry` · `Adiabatic_process` · `Agricultural_chemistry` · `Alchemy` · `Alcohol_dehydrogenase` · `Amateur_chemistry` · `Amazon_Standard_Identification_Number` · `Amino_acid` · `Analog_computer` · `Analysis_of_algorithms` · `Analytical_chemistry` · `Andersen_thermostat` · `Aneesur_Rahman` · `Anton_(computer)` · `Application-specific_integrated_circuit` · `Aqueous_solution` · [[Argon]] · `Arieh_Warshel` · `Astrochemistry` · `Atmospheric_chemistry` · `Atom` · `Atomic_radius` · `Bacteriophage` · `Barostat` · `Bcl-xL` · `Beeman's_algorithm` · `Berendsen_thermostat` · `Berni_Alder` · `Big_O_notation` · `Biochemistry` · `Biogeochemistry` · `Bioinorganic_chemistry` · `Biological_membrane` · `Bioorganic_chemistry` · `Bioorganometallic_chemistry` · `Bioorthogonal_chemistry` · `Biophysical_chemistry` · `Biophysics` · `Biosynthesis` · `Bond_length` · `Bond_order_potential` · `Born–Mayer_equation` · `Born–Oppenheimer_approximation` · `Buckingham_potential` · `Buffon's_needle_problem` · `C++` · `CASP` · `CHARMM` · `CPU_time` · `CUDA` · `C_(programming_language)` · `Calorimetry` · `Canonical_ensemble` · `Capsid` · 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`Cosmochemistry` · [[Coulomb's_law]] · `Cryochemistry` · `Crystallography` · `D._E._Shaw_Research` · `DNA` · `Daan_Frenkel` · `David_E._Shaw` · `De_novo_protein_structure_prediction` · `Density_functional_theory` · `Dihedral_angle` · `Discrete_element_method` · `Discretization_error` · `Drude_particle` · `Drug_design` · `Duke_University` · `Dynamic_covalent_chemistry` · [[Dynamics_(mechanics)]] · `Elastic_collision` · `Electroanalytical_methods` · `Electrochemistry` · `Electron_ionization` · `Electronvolt` · `Electrostatics` · `Elemental_analysis` · `Embedded_atom_model` · `Enantioselective_synthesis` · `Energy_minimization` · `Enrico_Fermi` · `Enthalpy` · [[Entropy]] · `Environmental_chemistry` · `Equilibrium_chemistry` · `Ergodic_hypothesis` · `Ewald_summation` · [[Fast_Fourier_transform]] · `Fast_multipole_method` · `Femtochemistry` · `Fermi–Pasta–Ulam–Tsingou_problem` · `Flying_ice_cube` · `Folding@home` · `Food_chemistry` · `Food_physical_chemistry` · `Force_field_(chemistry)` · 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[[Newton's_laws_of_motion]] · `Nicholas_Metropolis` · `Nobel_Prize` · `Nobel_Prize_in_Chemistry` · `Nosé–Hoover_thermostat` · `Nuclear_chemistry` · `Nuclear_magnetic_resonance_spectroscopy` · `Nucleic_acid` · `Numerical_analysis` · [[Numerical_integration]] · `Nvidia` · `OpenCL` · `Organic_chemistry` · `Organic_synthesis` · `Organolanthanide_chemistry` · `Organometallic_chemistry` · `P3M` · `Parallel_algorithm` · `Parallel_computing` · `Periodic_boundary_conditions` · `Periodic_table` · `Permittivity` · `Pharmacology` · `Pharmacophore` · `Phi_value_analysis` · `Photochemistry` · `Photoelectrochemistry` · `Photogeochemistry` · `Physical_chemistry` · `Physical_organic_chemistry` · `Polarizability` · `Polymer` · `Polymer_chemistry` · `Polymer_science` · `Post-mortem_chemistry` · `Potential_energy` · `Potential_energy_surface` · `Potential_of_mean_force` · `Protein` · `Protein_folding` · `Protein_structure` · `Protein_structure_prediction` · `QM/MM` · `Quantum_chemistry` · [[Quantum_mechanics]] · `Radiation_chemistry` · `Radiochemistry` · `Raman_spectroscopy` · `Random_coil` · `Reaction_coordinate` · `Reaction_field_method` · `ReaxFF` · `Receiver_operating_characteristic` · `Receptor_(biochemistry)` · `Retrosynthetic_analysis` · `Ribosome` · `Screened_Coulomb_potentials_implicit_solvent_model` · `Self-diffusion` · `Semisynthesis` · `Separation_process` · `Shifted_force_method` · [[Silicon]] · `Soil_chemistry` · `Solid-state_chemistry` · `Solvent` · `Sonochemistry` · `Spectroelectrochemistry` · `Spectroscopy` · `Spin_chemistry` · `Stability_of_the_Solar_System` · `Statistical_mechanics` · `Stellar_chemistry` · `Stereochemistry` · `Stoichiometry` · `Structural_biology` · `Structural_chemistry` · `Supramolecular_chemistry` · `Surface_science` · `Susan_Sinnott` · `Symplectic_integrator` · `Synthetic_molecular_motor` · `Tamar_Schlick` · `Temperature` · `The_central_science` · `Theoretical_chemistry` · `Theoretical_physics` · `Thermochemistry` · `Thermostat` · `Thin_film` · `Timeline_of_chemistry` · `Titration` · `Total_synthesis` · `Trajectory` · `Ultraviolet–visible_spectroscopy` · `Umbrella_sampling` · `University_of_Florida` · `University_of_Minnesota` · `University_of_Southern_California` · `VSEPR_theory` · `Vacuum_permittivity` · `Van_der_Waals_force` · `Verlet_integration` · `Verlet_list` · `Vienna_Ab_initio_Simulation_Package` · `Virus` · `Water_model` · `Wet_chemistry` · `X-ray_crystallography` · `Young's_modulus` ## Overview Molecular dynamics is a computer-simulation method for modelling the motion of atoms and molecules by numerically integrating Newton's equations of motion. Introduced by Berni Alder and Thomas Wainwright for hard spheres in the late 1950s and extended by Aneesur Rahman, whose 1964 study of liquid argon used a continuous Lennard-Jones potential, MD has become a core tool across chemistry, materials science, and structural biology. It bridges the microscopic world of forces and the macroscopic world of thermodynamics: from a single trajectory one can extract temperature, pressure, diffusion coefficients, and phase behaviour. Modern simulations track anywhere from a handful of atoms to billions, advancing over femtosecond (10⁻¹⁵ s) time-steps. ## The physics Each pair of particles interacts through the Lennard-Jones potential, V(r) = 4ε[(σ/r)¹² − (σ/r)⁶], whose steep r⁻¹² term models Pauli repulsion between overlapping electron clouds and whose r⁻⁶ term captures attractive van der Waals dispersion. The well has depth ε and reaches its minimum at r = 2^(1/6)σ ≈ 1.122σ. The force, F(r) = −dV/dr = (24ε/r)[2(σ/r)¹² − (σ/r)⁶], is summed over neighbours and fed to the velocity-Verlet integrator, which advances positions and velocities time-reversibly while conserving energy. Working in reduced units removes σ, ε, and mass m from the arithmetic: | Quantity | Reduced form | |---|---| | Length | r* = r/σ | | Energy | E* = E/ε | | Temperature | T* = k_B T/ε | | Density | ρ* = ρσ³ | | Time | t* = t·√(ε/mσ²) | Temperature is tied to kinetic energy by equipartition, ⟨½mv²⟩ = (d/2)k_B T per particle in d dimensions, so the thermostat holding the system at T₀ works by rescaling velocities toward that target. Fitting this model to real argon gives ε/k_B ≈ 120 K and σ ≈ 0.34 nm. The Lennard-Jones fluid's triple point sits near T* ≈ 0.69 and its critical point near T* ≈ 1.3 — landmarks you can straddle within the sim's ranges. ## Controls → what each maps to | Control | Maps to (symbol) | Range / values | Physical meaning | |---|---|---|---| | Particles N | N | 10–150 | Number of atoms in the box; sets statistics and cluster size | | density ρ | ρ* = Nσ³/V | 0.05–0.60 | Packing fraction; separates gas-like from liquid-like regimes | | target temperature T₀ | T (setpoint) | 0.05–3.00 | Thermostat target; jitter relative to well depth ε (T* = k_B T/ε) drives melting/freezing | | interaction strength ε | ε | 0.20–3.00 | Depth of the LJ well; strength of cohesion at fixed T₀ | | simulation speed | steps/frame | 1–8 | Integration steps per rendered frame; time throughput, not physics | ## Learning objective After playing, a learner can predict how changing density, temperature, or well depth moves a Lennard-Jones system between gas, liquid, and ordered-solid behaviour, and explain why those transitions arise from a single pair potential. ## Limits and connections The sim uses classical point particles with no quantum effects, chemical bonds, or long-range electrostatics, so it models noble-gas-like fluids rather than reacting molecules; real force fields add many-body and Coulomb terms. Even so, the same machinery underlies simulations of Nanomaterials, crystal nucleation, and the conformations of long chains in Polymer chemistry. ## Poster & source <div class="microsim-fallback">  <p><em>Live microsim · <a href="https://wikitube-3d-microsims.netlify.app/Molecular_dynamics.html">open full</a> · source: Microsims for Dissemination/REACTION/Molecular_dynamics.html</em></p> </div>  *Built to the [[WT!Three_js_Microsim_Master_Class|three.js Master Class]].*  ## Wikipedia : Wikitube **Strict pair:** [Wikipedia](https://en.wikipedia.org/wiki/Molecular_dynamics) : [Wikitube](https://en.wikitube.io/wiki/Molecular_dynamics) ## Previous hub tags Tree parents: [[Information_theory]] · [[Monte_Carlo_method]] · [[Phase_space]]. Legacy hubs: `REACTION`. --- *Sources: 1 legacy note. Minted wave 1, 2026-07-30 (v1.6 order).*