This repository contains molecular dynamics simulation setup files and analysis scripts used in the study "Hidden Structural States of Proteins Revealed by Conformer Selection" by Huang, Ramelot, Spaman, Kobayashi, and Montelione.

This repository contains molecular dynamics (MD) simulation setup files and analysis scripts used in the study “Hidden Structural States of Proteins Revealed by Conformer Selection” by Huang, Ramelot, Spaman, Kobayashi, and Montelione. The simulations were performed on Gaussia luciferase (GLuc) to characterize conformational states identified using the AISAR (AI Sampling with NMR Recall selection) framework. The archive includes all files required to reproduce the MD simulations, including coordinate files, topology files, GROMACS parameter files (.mdp), index files, and run scripts for six independent simulations representing two conformational states (three replicates per state). The simulations were performed using GROMACS with the AMBER99SB-ILDN force field and the TIP3P water model. Analysis scripts and processed data used to generate the MD-derived results reported in the manuscript are also included, together with example plots produced from the trajectory analyses. A detailed description of the simulation systems, including box dimensions, number of atoms, ion counts, thermostat and barostat parameters, and simulation lengths, is provided in SI_MD_Setup_Table.docx, which corresponds to the supplementary MD setup table included in the manuscript.