Protein Simulator Based on Quantized Oscillator Molecular Dynamics

Existing molecular dynamics simulation software depends on fixed molecular force field models, with insufficient flexibility in parameter adjustments. To address these issues, a novel molecular dynamics simulator based on quantized oscillators has been designed to study the full-atomic-scale motion of proteins. The principle is to treat the bonding interactions between protein atoms as elastic oscillators, combined with non-bonded charge interactions. The atomic displacement is quantized based on Hamiltonian mechanics. The adjustable set of charge and spectral parameters is based on the principles of quantum mechanical atomic and molecular orbital models. By calculating the charge forces of atomic interactions and the vibration spectra of elastic oscillators, and then parameterizing these interactions, an adjustable parameter set was derived. Experiments show that the simulator can model the full-atomic-scale motion of proteins, and by adjusting atomic charge and spectral parameters, dynamic simulations could be conducted under different conditions to meet specific observation goals. Temperature monitoring of the protein molecules reveals that the protein molecules maintain thermal stability throughout the simulation process.