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- W2913758340 abstract "In molecular dynamics (MD) simulations, an accurate evaluation of temperature and pressure is essential for controlling temperature as well as pressure in the isothermal-isobaric conditions. In MD, conventional approaches of temperature and pressure evaluations from kinetic energy do not include Hessian terms properly, and are not appropriate with a large time step. To enable an MD simulation with a large time step, we suggest more optimal temperature and pressure evaluations. Temperature is evaluated by combining two types of kinetic energies: kinetic energies defined at half- and full-time steps. Pressure is evaluated only from the kinetic energy at half-time step. These provide optimal instantaneous temperature and pressure up to the third order of the time step while conventional ones are accurate only up to the first order of the time step. The method is tested for a one-dimensional harmonic oscillator, pure water molecules, a Bovine pancreatic trypsin inhibitor (BPTI) protein in water molecules, and a hydrated 1,2-dispalmitoyl-sn-phosphatidylcholine (DPPC) lipid bilayer in water molecules. In all tests, our temperature/pressure evaluations well reproduce the usual physical properties for time steps up to 5 fs." @default.
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- W2913758340 date "2019-02-01" @default.
- W2913758340 modified "2023-09-28" @default.
- W2913758340 title "Optimal Temperature and Pressure Evaluations in Molecular Dynamics Simulations with a Large Time Step" @default.
- W2913758340 doi "https://doi.org/10.1016/j.bpj.2018.11.783" @default.
- W2913758340 hasPublicationYear "2019" @default.
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