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DiTe2: Calculating the diffusion tensor for flexible molecules.

Jonathan Campeggio1, Antonino Polimeno1, Mirco Zerbetto1

  • 1Department of Chemical Sciences, University of Padua, Padova 35131, Italy.

Journal of Computational Chemistry
|December 15, 2018
PubMed
Summary

This study introduces DiTe2, a software update for hydrodynamic modeling of molecular friction. It now includes stretching and bending motions, enhancing the simulation of flexible molecules like calmodulin.

Keywords:
Brownian dynamicscoarse grainingdiffusion tensorhydrodynamicsreaction coordinates

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Area of Science:

  • Computational chemistry
  • Molecular dynamics
  • Biophysics

Background:

  • Hydrodynamic modeling is crucial for understanding molecular motion.
  • Existing methods like DiTe primarily focused on dihedral angles for flexibility.
  • A need exists for more comprehensive modeling of internal molecular mobility.

Purpose of the Study:

  • To extend hydrodynamic modeling capabilities for flexible molecules.
  • To incorporate stretching and bending internal coordinates into friction tensor calculations.
  • To enable calculation of friction tensors along collective coordinates.

Main Methods:

  • Extended and updated the DiTe software to create DiTe2.
  • Implemented hydrodynamic modeling for generalized translational, rotational, and configurational friction and diffusion tensors.
  • Included stretching, bending, and dihedral angle internal mobilities.

Main Results:

  • DiTe2 successfully incorporates stretching and bending internal mobilities.
  • The software can calculate friction and diffusion tensors along collective coordinates.
  • Tests using calmodulin (all-atom and coarse-grained) demonstrate DiTe2's enhanced features.

Conclusions:

  • DiTe2 provides a more comprehensive tool for hydrodynamic modeling of flexible molecules.
  • The enhanced capabilities allow for more accurate simulations of molecular behavior.
  • This advancement aids in understanding the dynamics of complex biological systems.