About Me and This Page
I am a Chemistry graduate student at UT Arlington. This blog is meant to share articles, reading notes, and helpful coding snippets related to computational chemistry, biophysics, and allied topics...
Raafik's Page
Poster Presentation at 2024 CHARMM Developers Meeting and Gordon Research Conference
DISCLAIMER: The content in this article is for demonstration purposes only and may contain errors and technical inaccuracies. Exploring Transferability of Machine Learning Potentials for F...
Machine Learning Assisted QM/MM Free Energy Simulations: A Quick Way to Set up an Interface to Python in CHARMM
DISCLAIMER: The content in this article is for demonstration purposes only and may contain errors and technical inaccuracies. DISCLAIMER: The code modifications might not be looking clean a...
ACS-SWRM-2023: Dynamic Perspectives on Catalytic Function in Adenylate Kinase
DISCLAIMER: The content in this article is for demonstration purposes only and may contain errors and technical inaccuracies. This article aims to provide a concise overview of my presenta...
Lipari-Szabo $S^2$ Order Parameters from Molecular Dynamics Simulation Trajectories
DISCLAIMER: The content in this article is for demonstration purposes only and may contain errors and technical inaccuracies. This article discusses how molecular dynamics (MD) simulation t...
Statistics of Averages from Molecular Dynamics Trajectories: Time Auto-correlation Function
DISCLAIMER: The content in this article is for demonstration purposes only and may contain errors and technical inaccuracies. This article briefly discusses the theory behind calculating cor...
PyMOL-Python External Functions for CHARMM MD Trajectory Analysis
DISCLAIMER: The content in this article is for demonstration purposes only and may contain errors and technical inaccuracies This post is about how to do some quick analyses directly from pr...