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Computational Methods for Configurational Entropy Using Internal and Cartesian Coordinates.

Simon Hikiri1, Takashi Yoshidome1, Mitsunori Ikeguchi1

  • 1Graduate School of Medical Life Science, Yokohama City University , 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.

Journal of Chemical Theory and Computation
|December 14, 2016
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Summary
This summary is machine-generated.

The Boltzmann-quasi-harmonic (BQH) method using internal coordinates accurately calculates configurational entropy. This computational method, crucial for biophysical processes, outperforms others, especially with improper torsions.

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Area of Science:

  • Biophysics
  • Computational Chemistry
  • Molecular Dynamics

Background:

  • Configurational entropy is vital for understanding biophysical processes.
  • Accurate computational methods for calculating configurational entropy are needed.

Purpose of the Study:

  • To evaluate the performance of quasi-harmonic and related computational methods for calculating configurational entropy.
  • To compare these methods with the Clausius method and widely used molecular dynamics (MD) software packages.
  • To investigate the impact of coordinate systems (internal vs. Cartesian) on accuracy.

Main Methods:

  • Investigated Boltzmann-quasi-harmonic (BQH) method using internal coordinates.
  • Compared BQH with six other methods, including those in popular MD packages.
  • Utilized replica-exchange MD simulations for enhanced sampling.
  • Examined the effect of improper torsions and anharmonicity.

Main Results:

  • The BQH method using internal coordinates significantly outperformed all other examined methods.
  • Incorporating improper torsions improved BQH performance, attributed to protein torsion anharmonicity.
  • Widely used MD package methods showed poor performance.
  • Replica-exchange MD enhanced sampling improved entropy calculation convergence.
  • BQH was reasonably accurate for protein folding/unfolding transitions, with the independent term being most accurate for folding entropy.

Conclusions:

  • The BQH method with internal coordinates is a superior computational approach for calculating configurational entropy.
  • Protein torsion anharmonicity is key to the BQH method's enhanced performance.
  • Standard MD package methods are less reliable for configurational entropy calculations.
  • The BQH method shows promise for studying protein folding dynamics, though approximations may limit accuracy in highly divergent states.