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Stochastic Dynamics with Correct Sampling for Constrained Systems.

E A J F Peters1, N Goga2, H J C Berendsen2

  • 1Department of Chemical Engineering and Chemistry, Eindhoven University of Technology , P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.

Journal of Chemical Theory and Computation
|November 21, 2015
PubMed
Summary
This summary is machine-generated.

This study addresses temperature control in molecular simulations with constraints. New methods ensure accurate temperature regulation, even with limited particle selection, for reliable simulations like extended simple point charge (SPC/E) water.

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Area of Science:

  • Computational chemistry
  • Statistical mechanics
  • Molecular dynamics

Background:

  • Stochastic thermostatting methods are crucial for molecular simulations.
  • Impulsive thermostats can inaccurately control temperature when constraints are applied to limited particle sets.

Purpose of the Study:

  • To analyze and provide rigorous solutions for temperature inaccuracies in constrained molecular simulations using impulsive stochastic thermostats.
  • To develop a general treatment for stochastic thermostatting with constraints.

Main Methods:

  • Analysis of temperature deviations in constrained systems under impulsive thermostatting.
  • Development and application of two rigorous solutions for accurate temperature control.
  • Incorporation of pairwise dissipative particle dynamics and stochastic forcing.
  • Discussion of implementation details like second-order Trotter expansions.

Main Results:

  • Identified and solved the problem of temperature deviation in constrained simulations.
  • Demonstrated rigorous sampling of the constrained canonical distribution.
  • Validated the method's ability to maintain correct temperature in extended simple point charge (SPC/E) water simulations.

Conclusions:

  • The proposed methods provide accurate temperature control in molecular simulations with constraints.
  • This work offers a general and rigorous treatment for stochastic thermostatting in constrained systems.
  • The findings are crucial for reliable molecular simulations, particularly for systems like SPC/E water.