AmberMD-Scripting

AmberMD-Scripting is a small collection of Bash helpers for preparing and running staged AMBER molecular dynamics workflows. The repository is aimed at practical command-line usage rather than a general-purpose software package.

Repository contents

generate_amber_inputs.sh

Generates a directory tree and AMBER input files for a staged membrane-oriented workflow that includes:

• minimization
• restrained heating
• restrained equilibration
• production dynamics

The script builds numbered directories such as 001.min, 002.heat, and trajectory-specific folders like Traj1/003.equil and Traj1/004.prod.

Example:

bash generate_amber_inputs.sh 101 120 3

This generates inputs for 3 trajectories with ligand or residue restraints applied over residues 101 to 120.

A cleanup mode is also available:

bash generate_amber_inputs.sh cleanup 3

run_md_simulations.sh

Runs the generated AMBER workflow in either preproduction or production mode.

Example preproduction run:

bash run_md_simulations.sh system_name 16 0

Example production run:

bash run_md_simulations.sh system_name 16 1 0 0 5 1

This corresponds to:

• system_name = AMBER topology/restart basename
• 16 = number of CPU cores
• 1 = production mode
• 0 = GPU index
• 0 = starting production segment
• 5 = final production segment
• 1 = trajectory number

Workflow assumptions

These scripts assume:

• an AMBER installation with pmemd.MPI and pmemd.cuda
• an MPI launcher available as mpirun
• a membrane-style workflow using the directory structure created by generate_amber_inputs.sh
• topology and coordinate files such as system_name.parm7 and system_name.rst7

Scope and limitations

This repository is best viewed as a reusable lab-style scripting helper rather than a polished framework. The workflow reflects specific simulation assumptions, including staged restrained equilibration and membrane-oriented restraint setup, so users should review the generated input files before adopting them in a different context.

Contributing

Focused pull requests are preferred. The most useful contributions are bug fixes, clearer usage notes, portability improvements, and workflow clarifications that preserve the repository’s lightweight scripting focus.

Citation

If this repository contributes to published work, please cite the repository and the version used.

License

This project is released under the MIT License. See LICENSE for details.

Contact

For questions or adaptation to related workflows, see the repository owner profile: https://github.com/fr-0zt