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molecular dynamics

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atom molecule simulation trajectory potential energy kinetics thermodynamics Newtonian mechanics integration velocity acceleration position ensemble canonical isothermal isobaric temperature pressure volume entropy enthalpy Maxwell collision diffusion viscosity conformation folding protein peptide ligand binding affinity solvent water hydration solvation periodic boundary cutoff electrostatics Coulomb bond angle dihedral torsion constraint algorithm leapfrog thermostat equilibrium ergodic fluctuation correlation spectroscopy crystallography biophysics computational modeling quantum hybrid sampling Monte Carlo free energy landscape transition state activation energy hydrogen bond hydrophobicity

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