Scripts

Recopilation of different scripts used for my MD analysis

AnalysisCpptraj

Contains bash scripts with cpptraj commands inside Parameters to be passed are name conventions of my files

Python scripts to analyze MD data. Automatize as well the production of plots.

Inputs for the MD simulations and PBS/Bash scripts to run the jobs in HPC or local machines with GPUs

Starting to use Python scripts to implement MSM analysis on MD data using MSMbuilder/MDtraj

R commands to produce plots from analysis of MD data usually coming from cpptraj analysis.

Dotfiles or other stuff that doesn't fit in any of the categories above

Name		Name	Last commit message	Last commit date
Latest commit History 284 Commits
.ipynb_checkpoints		.ipynb_checkpoints
AnalysisCpptraj		AnalysisCpptraj
AnalysisMDTraj		AnalysisMDTraj
Chimera_Presets		Chimera_Presets
MDinputs		MDinputs
MSManalysis		MSManalysis
Rplots		Rplots
misc		misc
.gitignore		.gitignore
LICENSE		LICENSE
README.md		README.md
StateFile		StateFile
add_preceding0.py		add_preceding0.py
average_trajectoryChimera.py		average_trajectoryChimera.py
create_Gaussian_scripts.py		create_Gaussian_scripts.py
dist_plot.sh		dist_plot.sh
distances_percent.py		distances_percent.py
do_hmr.sh		do_hmr.sh
do_network_adaptive_trajs.py		do_network_adaptive_trajs.py
do_strips_autoimage.sh		do_strips_autoimage.sh
firstcolumn_multiply.sh		firstcolumn_multiply.sh
gaussian_parsing.py		gaussian_parsing.py
kde_compare.py		kde_compare.py
kde_juan.py		kde_juan.py
load_big_trajs.sh		load_big_trajs.sh
load_ctf_vmd.sh		load_ctf_vmd.sh
load_troponin_vmd.sh		load_troponin_vmd.sh
min_image.py		min_image.py
name_changer.py		name_changer.py
notebook.mplstyle		notebook.mplstyle
notebook_essentials.py		notebook_essentials.py
reduce_pdf_size.sh		reduce_pdf_size.sh
rename_np_arrays.py		rename_np_arrays.py
source_sinks_chimera.cmd		source_sinks_chimera.cmd
strip_H1P.sh		strip_H1P.sh
strip_autoimage.sh		strip_autoimage.sh
tica_array.py		tica_array.py
tidy_markdown.py		tidy_markdown.py
timeLabel_chimera.py		timeLabel_chimera.py
traj_length.sh		traj_length.sh
workspace.sh		workspace.sh