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Force probe simulations using an adaptive resolution scheme.

Marco Oestereich1, Jürgen Gauss1, Gregor Diezemann1

  • 1Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany.

Journal of Physics. Condensed Matter : an Institute of Physics Journal
|March 10, 2021
PubMed
Summary

Multiscale simulations using adaptive resolution (AdResS) accelerate force probe molecular dynamics (FPMD) by reducing computational cost. This hybrid approach accurately captures biomolecular unfolding dynamics even under strong non-equilibrium conditions.

Keywords:
coarse grainingforce probe simulationshybrid simulations

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Area of Science:

  • Computational Chemistry
  • Biophysics
  • Molecular Dynamics

Background:

  • Molecular simulations provide insights into biomolecular folding dynamics and energy landscapes.
  • Force probe molecular dynamics (FPMD) simulations are computationally intensive due to solvent requirements.

Purpose of the Study:

  • To investigate the applicability of multiscale simulations with the adaptive resolution scheme (AdResS) to FPMD simulations.
  • To compare AdResS-based FPMD simulations with all-atom simulations for accuracy and efficiency.

Main Methods:

  • Applied a hybrid multiscale approach combining atomistic resolution for the solute and coarse-grained resolution for distant solvent molecules.
  • Utilized the adaptive resolution scheme (AdResS) for FPMD simulations of mechanically interlocked calixarene capsules.
  • Compared results with traditional all-atom FPMD simulations.

Main Results:

  • AdResS-based FPMD simulations successfully captured conformational transitions during forced unfolding.
  • The required size of the atomistic region in AdResS was found to be dependent on the pulling velocity.
  • Larger atomistic regions were necessary for higher pulling velocities in non-equilibrium simulations.

Conclusions:

  • Multiscale simulations using AdResS are effective for FPMD, even in strong non-equilibrium scenarios.
  • The adaptive resolution approach offers a computationally efficient alternative to all-atom simulations for studying biomolecular dynamics.