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.