Molecular Dynamics Simulations with AMBER
In this repository, you'll find two shell scripts designed to perform Molecular Dynamics (MD) simulations using the AMBER suite of programs.
The first script, generate_amber_inputs.sh, creates the required input files for AMBER simulations. It enables the generation of multiple trajectories with ligand constraints specified by a range of residues.
The second script, run_md_simulations.sh, executes preproduction or production MD simulations on a specified system using the AMBER suite of programs.
To use these scripts, follow these steps:
- Generate the necessary input files by running generate_amber_inputs.sh with the desired parameters:
./generate_amber_inputs.sh [RESIDUE_START] [RESIDUE_END] [NUMBER_OF_TRAJECTORIES]
- Run the MD simulations by executing run_md_simulations.sh with the appropriate arguments:
./run_md_simulations.sh [SYSTEM NAME] [CPU] [0/1] [GPU INDEX] [MD Start] [MD Stop]
For more detailed instructions on how to use these scripts, please refer to the comments in each script.