# Simulation Workflow
This directory contains a complete Molecular Dynamics (MD) simulation pipeline.

- 1_build   : Generate the system topology (wbox.prmtop) and initial coordinates (wbox.inpcrd).
- 2_minimize: Perform energy minimization to relieve steric clashes.
- 3_heat    : Gradually heat the system from 0 K to the target temperature (defined in heat.in).
- 4_equil   : Conduct a short equilibration run (e.g., 1 ns) using production-level settings to stabilize the system.
- 5_run     : Execute the production run for data collection (e.g., 1 µs).

# Helper Scripts
Utility scripts for job management and environment configuration.

- chgpu.sh: Designate the GPU device for the simulation.
    Usage: `./chgpu.sh 2` (sets GPU index to 2).
- clean_all.sh: Remove all intermediate and output files from the simulation directories.
    Usage: `./clean_all.sh`
- run.sh: Execute specific simulation stages.
    Usage: Modify the file first. `./run.sh` will run the wanted stages.

# Others
Supplementary materials and post-processing tools.

- amber_demo: Sample input PDB files (selected frames with mutations).
- process: Scripts for trajectory post-processing, analysis, and visualization.
