André Guerra
July, 2022
[email protected]
Description:
This is repository contains an introduction to molecular dynamics (MD) simulations using PACKMOL, Moltemplate, and LAMMPS. I have tried to demonstrate a workflow for simulating a simple system. This workflow can be modified and extented as desired for your project. The system molecule coordinates are defined in 1_packmol, and the PACKMOL software is used to populate a simulation box. Next, the system's data file is generated with Moltemplate in 2_moltemplate. Finally, the LAMMPS simulation is conducted in 3_lammps. This tree structure is designed to contain the workflow, segregate files used/produced by different software packages, and ultimately to organize our project space. The bash script run.sh executes the workflow.
Below you will see a list of the contents of the repository. The markdown file main.md will be the hub where all information regaring this molecular dynamics workshop is found. So, let's continue this over there!
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1_packmol/$\rightarrow$ files associated with PACKMOL -
2_moltemplate$\rightarrow$ files associated with Moltemplate -
3_lammps$\rightarrow$ files associated with LAMMPS -
main.md$\rightarrow$ this file contains the main content of this workshop -
run.sh$\rightarrow$ bash script that runs the MD workflow -
run_cvmfs.sh$\rightarrow$ modified bash script that runs the MD workflow on a cluster with slurm scheduler and the CVMFS stack (for reference and for my own testing)