Self-consistent coupling of molecular theory of solvation with - - PowerPoint PPT Presentation

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Self-consistent coupling of molecular theory of solvation with - - PowerPoint PPT Presentation

Feb 21, 2024 268 likes •373 views

Self-consistent coupling of molecular theory of solvation with molecular simulations Presented by: CAO Siqin, Jan 7 Solvate with 3D-RISM-KH Bridge between solvation theory and other methods: = + Solvate with 3D-RISM-KH: Andriy Kovalenko and

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Presented by: CAO Siqin, Jan 7

Self-consistent coupling of molecular theory of solvation with molecular simulations

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Solvate with 3D-RISM-KH

Andriy Kovalenko and Sergey Gusarov, Phys. Chem. Chem. Phys. 20, 2947 (2018)

Bridge between solvation theory and other methods: = + Solvate with 3D-RISM-KH:

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MTS-MD/OIN/GSFE/3D-RISM-KH

Andriy Kovalenko and Sergey Gusarov, Phys. Chem. Chem. Phys. 20, 2947 (2018)

  • MTS: multi-timescale
  • MD: molecular dynamics
  • OIN: optimized isokinetic Nosé–Hoover
  • GSFE: generalized solvation force extrapolation
  • 3D-RISM-KH: 3D reference interaction site model

complemented with the Kovalenko-Hirata closure Chain-thermostat Total force Kinetics

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MTS-MD/OIN/GSFE/3D-RISM-KH: GSFE

Andriy Kovalenko and Sergey Gusarov, Phys. Chem. Chem. Phys. 20, 2947 (2018)

Solvation force: Solvation force extrapolation, the GSFE (general solvation force extrapolation): Coupling Scheme Translation Perform 3D-RISM every h Extrapolate force every Δt Vacuum kinetics otherwise

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How does it save time

Andriy Kovalenko and Sergey Gusarov, Phys. Chem. Chem. Phys. 20, 2947 (2018)

h MTS-MD Speedup

  • 1 ns/day
  • 8 fs

0.15 ns/day 15% 24 fs 0.44 ns/day 44% 400 fs speedup grows slowly 1 ps 10 ns/day 10x 2~4 ps speedup saturated

* Fitting of speedups: speedup = 0.1366 + 0.00986×h/(1 fs) * 3D-RISM: 1 step RISM ≈ 51 steps explicit solvent MD

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Problem with the implicit-solvent MD

[1] my understanding [2] Andriy Kovalenko and Sergey Gusarov, Phys. Chem. Chem. Phys. 20, 2947 (2018)

Protein Conformation Protein Conformation Solvent Configuration Solvent Configuration Explicit Solvent MD Implicit Solvent MD miniprotein 1L2Y protein G Thermodynamics could be correct Kinetics could be wrong Folding time: 60 ns (MD) vs 4-9 us (Experiment)

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Alternatively, if only cares about thermodynamics ...

Hiroshi Iwasaki, Shinnosuke Gyoubu, Tsutomu Kawatsu and Shinichi Miura, Molecular Simulation 41, 1015-1020 (2014), Molecular Simulation 43, 997-1003 (2017)

Alanine dipeptide in vacuum solvated with 3D-RISM

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Summary

  • A. Kovalenko and S. Gusarov, Phys. Chem. Chem. Phys. 20, 2947 (2018); H. Iwasaki, S. Gyoubu, T. Kawatsu and S.

Miura, Molecular Simulation 41, 1015-1020 (2014), Molecular Simulation 43, 997-1003 (2017)

  • Implicit solvent MD with 3D-RISM:
  • 3D-RISM is too slow, so extrapolation is required
  • Conformation of proteins can be correct
  • Kinetics is incorrect
  • An alternative scheme: solvate the vacuum free energy

landscape with 3D-RISM