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Na-Cl Interaction Testing for NBFIX and NBTHOLE

This folder contains scripts and resources for testing the NBFIX and NBTHOLE parameters for Na-Cl interactions.

Contents

  • run_charmm.sh: Script to run the CHARMM test.
  • run_openmm.sh: Script to run the OpenMM test.
  • bench_mark: File containing benchmark data for performance and accuracy comparisons.

How to Run the Tests

To execute the tests, follow these steps:

  1. Ensure all required dependencies for CHARMM and OpenMM are installed.

  2. Make the scripts executable:

    chmod +x run_charmm.sh run_openmm.sh

  3. Run the CHARMM and OpenMM tests with the following commands:

    ./run_charmm.sh
./run_openmm.sh

Viewing Benchmark Results

The bench_mark file contains benchmark data for comparison.

Results

Results are written in

  • Result_CHARMM.txt: CHARMM result
  • Result_OPENMM.txt: OPENMM result

Due to variations in values across different software, we have established a relatively lenient pass criterion: an energy difference of less than 0.1 kcal/mol. If NBFIX or NBTHOLE is ineffective, the energy difference will be significantly higher.