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Fast reactions occurring in times shorter than the time needed to mix reactants pose a unique challenge for investigation. In a liquid-phase continuous-flow system, reactants A and B are swiftly pushed into the mixing chamber, where mixing occurs within 1 ms. The reaction mixture then flows through an observation tube, and one measures light absorption to determine species concentrations at various points of the tube. This method is most appropriate when relatively large volumes of reactants...
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Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics.

Levi C T Pierce1, Romelia Salomon-Ferrer, Cesar Augusto F de Oliveira

  • 1Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, Urey Hall, La Jolla, California 92093-0365, United States.

Journal of Chemical Theory and Computation
|September 18, 2012
PubMed
Summary

Accelerated molecular dynamics (aMD) on GPUs effectively samples millisecond protein dynamics. This enhanced sampling method, applied to BPTI, matches brute force simulations, offering routine access to rare events.

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Area of Science:

  • Computational Biology
  • Biophysics
  • Molecular Dynamics

Background:

  • Investigating slow protein conformational changes (millisecond timescale) is computationally challenging.
  • Enhanced sampling methods aim to accelerate the exploration of protein dynamics.

Purpose of the Study:

  • To assess the efficacy of all-atom accelerated molecular dynamics (aMD) for simulating millisecond protein dynamics.
  • To implement and evaluate aMD on graphics processing units (GPUs).

Main Methods:

  • Utilized all-atom accelerated molecular dynamics (aMD) simulations.
  • Combined aMD with GPU acceleration for enhanced computational performance.
  • Applied the method to the bovine pancreatic trypsin inhibitor (BPTI) protein.

Main Results:

  • A 500 ns aMD simulation on GPUs sampled the same conformational space as a millisecond unbiased simulation.
  • This work represents the first GPU implementation of aMD and the longest biomolecular aMD simulation to date.
  • The aMD implementation is publicly available in the Amber software suite.

Conclusions:

  • GPU-accelerated aMD is a powerful tool for exploring millisecond protein dynamics.
  • This approach provides routine access to rare conformational events using standard hardware.
  • The availability of this method facilitates broader research in protein dynamics.