MD simulations template

This is a template/example of a pipeline for MD simulations in gromacs and their analysis

Environment installation

for Mac there is a conda version

git clone git@github.com:intbio/conda.git
conda install -c conda-forge -c "file:/$PWD/conda" vmd=1.9.3

Alternatively, just install it manually into specific conda env.

Name		Name	Last commit message	Last commit date
Latest commit History 152 Commits
GMX_system		GMX_system
MDProtocols		MDProtocols
Run_scripts		Run_scripts
VMD_scripts		VMD_scripts
results		results
.gitignore		.gitignore
0_analyze_pdb.ipynb		0_analyze_pdb.ipynb
1KX5.pdb		1KX5.pdb
1_1_prepare_system.ipynb		1_1_prepare_system.ipynb
1_2_restraints.ipynb		1_2_restraints.ipynb
2_min_equil.ipynb		2_min_equil.ipynb
3_benchmarking.ipynb		3_benchmarking.ipynb
4_production_run.ipynb		4_production_run.ipynb
5_trj_preprocessing.ipynb		5_trj_preprocessing.ipynb
5_trj_preprocessing.sh		5_trj_preprocessing.sh
6_0_quality_control.ipynb		6_0_quality_control.ipynb
6_1_basic_analysis.ipynb		6_1_basic_analysis.ipynb
7_plumed_cv_analysis.ipynb		7_plumed_cv_analysis.ipynb
8_plumed_WTmetad_t1wtmd2_DNA_torsion.ipynb		8_plumed_WTmetad_t1wtmd2_DNA_torsion.ipynb
8_plumed_metad.ipynb		8_plumed_metad.ipynb
LOG.md		LOG.md
README.md		README.md
config.py		config.py
cron.sh		cron.sh
cutting.jpg		cutting.jpg
funcs.py		funcs.py
get_files.sh		get_files.sh
h3-h4_tm_DNA.pdb		h3-h4_tm_DNA.pdb
mol_geom.py		mol_geom.py
status.ipynb		status.ipynb
untitled.txt		untitled.txt
vdwradii.dat		vdwradii.dat
view_nucl.py		view_nucl.py
xpm_plot.py		xpm_plot.py
xvg_plot.py		xvg_plot.py