README

This is a brief overview of the simulations and the analysis. Note that there is some redundency in the files.

Simulation

setup.py

-Script to run MELD simulation for calmodulin (Trial3). All necesary restraint files are included.

-See github.com/maccallumlab/meld for more information on running MELD.

job.sh

Submits MELD simulation to cluster. Requires simultaneous access to 48 GPUs with CUDA.

See github.com/maccallumlab/meld for more information on running MELD.

rest_files

Contains restraint files for PRE-derived restraints (split by location and distance)

Analysis

Clustering

mdrmsd.py

Clustering protocol. HDBSCAN with min_cluster_size=200

Input	Description
cam_fill.pdb	PDB of native
CaM_Trial{}.dcd	DCD of trajectory generated using meld "extract_trajectory extract_traj_dcd Cam_Trial{}.dcd --start=0 --end=50000"
trajectory_1.pdb	PDB of first frame of trajectory.pdb generated manually (functions as topology file)

Output	Description
k-dist.png	Visualized k-dist to help determine min_cluster_size
clusters_0{}.dat	RMSDs of clusters
cluster_0{}.pdb	PDBs of clusters

plot_rmsd.py

Generates histograms of clusters.

Input	Description
clusters_0{}.dat	RMSDs of clusters (from mdrmsd.py)

Output	Description
clusters_200h.png	Histogram image

KDE

get_rmsds.py

Determines rmsds to native for plotting KDEs (partially redundant, easier to use when only plotting KDEs than mdrmsd.py).

Excludes flexible tails, includes peptide.

Input	Description
cam_fill.pdb	PDB of native
CaM_Trial{}.dcd	DCD of trajectory generated using meld "extract_trajectory extract_traj_dcd Cam_Trial{}.dcd --start=0 --end=50000"
trajectory_1.pdb	PDB of first frame of trajectory.pdb generated manually (used as topology file)

Output	Description
rmsds_Trial{}.dat	RMSDs of native to each frame in trajectory (1 microsecond)

plot_kde.py

Plots KDEs using .dat files from get_rmsds.py. Bandwidth of 0.1 for smoothness.

Input	Description
rmsds_Trial{}.dat	RMSDs of native to each frame in trajectory (1 microsecond) (from get_rmsds.py)

Output	Description
kde_01_{}.png	KDE plot