2016/01/31 by Xingyu Gao, Jun Fang, Han Wang · 22 citations
Biochemistry, Genetics and Molecular Biology · Engineering · Materials Science · Mathematics · Physics and Astronomy · #Applied mathematics #Computer science #Coupling (piping) #Engineering #Isobaric process #Isothermal process #Langevin dynamics #Langevin equation #Material Dynamics and Properties #Mathematics #Mechanical engineering #Molecular dynamics #Nanopore and Nanochannel Transport Studies #Physics #Propagator #Protein Structure and Dynamics #Quantum mechanics #Statistical physics #Thermodynamics #cond-mat.stat-mech
paper · pdf · doi:10.1063/1.4944909
published in The Journal of Chemical Physics 144(12), 124113 (American Institute of Physics)
openalex publication_date 2016/03/28 · arxiv created 2016/04/27 · arxiv updated 2016/04/28 · openalex created_date 2016/06/24 · openalex updated_date 2026/08/05
We present a new method of conducting fully flexible-cell molecular dynamics simulation in isothermal-isobaric ensemble based on Langevin equations of motion. The stochastic coupling to all particle and cell degrees of freedoms is introduced in a correct way, in the sense that the stationary configurational distribution is proved to be consistent with that of the isothermal-isobaric ensemble. In order to apply the proposed method in computer simulations, a second order symmetric numerical integration scheme is developed by Trotter's splitting of the single-step propagator. Moreover, a practical guide of choosing working parameters is suggested for user specified thermo- and baro-coupling time scales. The method and software implementation are carefully validated by a numerical example.