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  1. Home
  3. Quick And Robust Esp And Resp Charges For Computational Biochemistry: Open-source Gpu Implementation.
  1. Home
  3. Quick And Robust Esp And Resp Charges For Computational Biochemistry: Open-source Gpu Implementation.

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QUICK and Robust ESP and RESP Charges for Computational Biochemistry: Open-Source GPU Implementation.

Vikrant Tripathy1, Etienne Palos2, Kenneth M Merz3,4

  • 1San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States.

Journal of Chemical Information and Modeling
|March 6, 2026

View abstract on PubMed

Summary
This summary is machine-generated.

We developed a new GPU-accelerated method for calculating electrostatic potential (ESP) charges, achieving significant speedups and robust molecular charge calculations. This method enhances molecular modeling and parametrization for force fields.

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Area of Science:

  • Computational Chemistry
  • Molecular Modeling
  • High-Performance Computing

Background:

  • Accurate partial charges are crucial for molecular simulations and force field parametrization.
  • Traditional electrostatic potential (ESP) charge calculations can be sensitive to molecular orientation and grid density.
  • Existing methods often lack robustness and efficiency for large-scale applications.

Purpose of the Study:

  • To implement highly efficient ab initio electrostatic potential (ESP) calculations on graphics processing units (GPUs).
  • To introduce a novel partial charge scheme robust against molecular orientation.
  • To enable ultradense-grid ESP computations for improved accuracy and reliability.

Main Methods:

  • Implementation of ESP calculations on GPUs using the Quantum Interaction Computational Kernel (QUICK) code.
  • Development of a reweighted RESP (rwRESP) charge scheme to overcome sensitivity to grid point number.
  • Performance analysis comparing GPU and CPU computational times.
  • Validation of charge robustness against molecular orientation.

    • Main Results:

    • A single data center GPU outperforms 128 CPU cores in ESP calculation time.
    • Ultradense-grid ESP computations (∼20000 points/atom) achieve orientation independence.
    • The novel rwRESP charge scheme demonstrates robustness against molecular orientation and grid density.
    • Seamless integration of QUICK with AmberTools facilitates parametrization of GAFF for nonstandard residues.

    Conclusions:

    • The GPU-accelerated protocol provides highly efficient and robust molecular charge calculations.
    • This method facilitates high-throughput parametrization and GPU-accelerated polarizable QM/MM simulations.
    • The developed protocol serves as a foundational step for advanced molecular modeling applications.