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At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
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Molecular dynamics simulations require unwrapping schemes to correct particle trajectories. A new hybrid unwrapping method corrects artifacts from changing box sizes, ensuring accurate molecular geometries in long simulations.

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Area of Science:

  • Computational Chemistry
  • Molecular Dynamics Simulations
  • Biophysics

Background:

  • Molecular dynamics (MD) simulations are crucial for studying nanoscale interactions.
  • Finite system sizes and periodic boundary conditions (PBCs) in MD simulations can introduce artifacts.
  • Trajectory unwrapping is essential for post-processing MD data to obtain continuous particle paths.

Purpose of the Study:

  • To evaluate existing trajectory unwrapping schemes for molecular dynamics simulations.
  • To identify and correct artifacts introduced by current unwrapping methods, particularly those related to changing periodic box dimensions.
  • To develop a robust unwrapping algorithm for accurate analysis of long molecular dynamics trajectories.

Main Methods:

  • Application of two established trajectory unwrapping schemes to 1 μs wrapped trajectories of water and lysozyme systems.
  • Development of a novel hybrid unwrapping algorithm incorporating a correction term for dynamic box size changes.
  • Implementation of the new unwrapping scheme in multiple periodic boundary condition handling tools.

Main Results:

  • Existing unwrapping schemes produced spurious diffusion coefficients and molecular geometry distortions.
  • The new hybrid unwrapping scheme successfully corrected artifacts caused by changing periodic box dimensions.
  • Molecular geometries remained accurate even after extended simulation times using the improved unwrapping method.

Conclusions:

  • Standard trajectory unwrapping methods are insufficient for accurate analysis of molecular dynamics simulations with dynamic box sizes.
  • The newly developed hybrid unwrapping algorithm provides accurate molecular geometries and physical properties.
  • This enhanced unwrapping approach is vital for reliable analysis of long molecular dynamics trajectories and is implemented for broader use.