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Optimized Hydrogen Mass Repartitioning Scheme Combined with Accurate Temperature/Pressure Evaluations for Thermodynamic and Kinetic Properties of Biological Systems.
Jung, Jaewoon; Kasahara, Kento; Kobayashi, Chigusa; Oshima, Hiraku; Mori, Takaharu; Sugita, Yuji.
Afiliación
  • Jung J; Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
  • Kasahara K; Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
  • Kobayashi C; Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 6-7-1 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
  • Oshima H; Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
  • Mori T; Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 6-7-1 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
  • Sugita Y; Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
J Chem Theory Comput ; 17(8): 5312-5321, 2021 Aug 10.
Article en En | MEDLINE | ID: mdl-34278793
In recent years, molecular dynamics (MD) simulations with larger time steps have been performed with the hydrogen-mass-repartitioning (HMR) scheme, where the mass of each hydrogen atom is increased to reduce high-frequency motion while the mass of a non-hydrogen atom bonded to a hydrogen atom is decreased to keep the total molecular mass unchanged. Here, we optimize the scaling factors in HMR and combine them with previously developed accurate temperature/pressure evaluations. The heterogeneous HMR scaling factors are useful to avoid the structural instability of amino acid residues having a five- or six-membered ring in MD simulations with larger time steps. It also reproduces kinetic properties, namely translational and rotational diffusions, if the HMR scaling factors are applied to only solute molecules. The integration scheme is tested for biological systems that include soluble/membrane proteins and lipid bilayers for about 200 µs MD simulations in total and give consistent results in MD simulations with both a small time step of 2.0 fs and a large, multiple time step integration with time steps of 3.5 fs (for fast motions) and 7.0 fs (for slower motions). We also confirm that the multiple time step integration scheme used in this study provides more accurate energy conservations than the RESPA/C1 and is comparable to the RESPA/C2 in NAMD. In summary, the current integration scheme combining the optimized HMR with accurate temperature/pressure evaluations can provide stable and reliable MD trajectories with a larger time step, which are computationally more than 2-fold efficient compared to the conventional methods.
Asunto(s)

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Simulación de Dinámica Molecular / Hidrógeno / Membrana Dobles de Lípidos / Proteínas de la Membrana Idioma: En Revista: J Chem Theory Comput Año: 2021 Tipo del documento: Article País de afiliación: Japón Pais de publicación: Estados Unidos

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Simulación de Dinámica Molecular / Hidrógeno / Membrana Dobles de Lípidos / Proteínas de la Membrana Idioma: En Revista: J Chem Theory Comput Año: 2021 Tipo del documento: Article País de afiliación: Japón Pais de publicación: Estados Unidos