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Infinite switch simulated tempering in force (FISST).

Michael J Hartmann1, Yuvraj Singh1, Eric Vanden-Eijnden2

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This study presents a new computational method to efficiently analyze how proteins respond to tiny forces. The technique allows researchers to simulate and understand protein behavior under various forces simultaneously, aiding in drug discovery.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Molecular Dynamics

Background:

  • Proteins sense and respond to piconewton-scale forces, crucial for biological functions.
  • Existing enhanced sampling methods are needed to study these force-induced conformational changes effectively.

Purpose of the Study:

  • To derive, implement, and evaluate an efficient method for simultaneously sampling molecular systems under a range of constant pulling forces.
  • To provide an enhanced sampling tool for studying force-induced protein dynamics, especially when forces destabilize low-free-energy states.

Main Methods:

  • Developed a method based on simulated tempering in force, adding force as a bias to the system's Hamiltonian.
  • Derived a formula for average force-dependent observables using on-the-fly learned weights.
  • Utilized the infinite switch limit for efficient sampling, analogous to temperature tempering.

Main Results:

  • Demonstrated accurate simultaneous sampling of molecular systems across a user-defined force range.
  • Showcased the method's utility in studying systems where pulling forces alter free-energy landscapes.
  • The technique allows retroactive computation of averages at any force within the simulated range.

Conclusions:

  • The new method provides efficient enhanced sampling for studying piconewton forces on molecular systems.
  • It enables a comprehensive analysis of force-response relationships in proteins.
  • The method is implemented in the PLUMED library, facilitating broad application in molecular dynamics simulations.