Convergence analysis and Input/Output files of molecular dynamics simulations of the Collagen Hydroxylysine Galactosyltransferase protein (GLT25D1/COLGALT1)

The directory contains a subdirectory named "input-out-coordinates-and-sim-input-files", which includes the input files for the molecular dynamics  simulations prod.in, as well as all the initial (GT*-*-replica-*-initial-coordinates.rst) and final coordinate files (GT*-*-replica-*-final-coordinates.rst) from the three independent replicates performed for each system.

The data are organized into two main folders: GT1 and GT2, corresponding to the two simulated domains. Within each of these folders, there are two subdirectories containing the plots of the analyses performed for the bound (HOLO) and unbound (APO) states of the system.

More specifically, each subdirectory contains:

RMSD time evolution plots:

rmsd_backbone_*-*.png: Root-mean-square deviation (RMSD) of the entire protein backbone over time for the three replicates of each corresponding system.

rmsd_backbone-*-*-no_terminals.png: RMSD of the protein backbone excluding the flexible terminal regions for the three replicates of each corresponding system.

Block-averaged RMSD analysis plots, named block_averaging-GT*-*-replica-*.png:  These figures show the block-averaged RMSD analysis for each independent replica, assessing the convergence of the simulations.

Additionally, the directory includes two Excel files:

Raw_data_time_course_analysis-RMSD.xlsx: This file contains 12 sheets, each providing the numerical data used to generate the RMSD time evolution plots and the  block-averaged RMSD analysis plots found in the corresponding system-specific subdirectories.

RMSD Block Averaging - Mean and Standard Error.xlsx: This file presents a summary table of the block-averaged RMSD values, including:

The mean RMSD computed over the selected blocks.

The standard error of the mean, which provides an estimate of the variability of the RMSD values across the blocks.