Welcome to the repository of Python scripts tailored for computational molecular dynamics.
As you explore and utilize these tools, we strongly recommend running them within a controlled Python environment, such as Conda.
This practice ensures that the necessary dependencies are managed effectively, minimizing conflicts and maintaining consistency across various projects.
Each script in this collection serves a specific purpose, from data analysis to simulation preprocessing, and is designed with the scientific community in mind. Please read the descriptions carefully, follow the usage instructions, and consider backing up your data before executing any script, as this will safeguard against unintended modifications.
Do open each file in a text editor to read the comments and understand the code. Make the edits you see fit for your use case. Never run someone eles's codes blindly!
Enjoy the streamlined workflow that these scripts are intended to provide!
RenamePDF.py
I often downloaded many (say 10-20) research papers with confusing names and had to rename them one by one to their actual titles. To save time, I wrote a script that does this automatically.
gpu_usages.py
Before running Gromacs simulations on my desktop, I would try different computing resources to see the GPU usage and simulation speed in ns/day. However, since nvidia-smi only showed the GPU usage at a single moment, I wrote a script that plots the GPU usage over the duration of the simulation.
For more information on monitoring simulation performance, visit the
GROMACS user guide.
NOTE: I write codes for my own convenience. I am sharing them here for the benefit of others. I am not responsible for any file loss or mishappening. Please use them at your own risk.