Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation,
Jing Huang1, Justin A Lemkul1, Peter K Eastman2
1Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Baltimore, Maryland, 21201.
Journal of Computational Chemistry
|May 5, 2018
Summary
The Drude force field is now accessible on GPUs via OpenMM, making complex polarizable simulations practical. This implementation significantly lowers the computational barrier for microsecond-scale molecular dynamics simulations.
Area of Science:
- Computational chemistry and molecular dynamics simulations.
- Development of efficient algorithms for molecular modeling.
Background:
- The Drude force field models electronic degrees of freedom using charged particles and virtual sites.
- This model introduces significant computational overhead compared to additive force fields.
- Previous limitations included the high computational cost for practical simulations.
Discussion:
- Implementation of the Drude force field within the OpenMM simulation package.
- Leveraging graphical processing unit (GPU) hardware for accelerated computations.
- Addressing the computational demands of the Drude model, including extra particles, virtual sites, and integration algorithms.
Key Insights:
- The Drude model implementation results in approximately a fourfold increase in computational demand.
- Accessibility to consumer-grade desktop GPU hardware enables microsecond-scale simulations in under a month.
- The practical barrier to employing polarizable models has been substantially reduced.
Outlook:
- Facilitates widespread adoption of polarizable simulations using the classical Drude model.
- Enables more accurate molecular modeling for complex chemical systems.
- Opens avenues for enhanced drug discovery and materials science research through accessible polarizable simulations.
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