########################################
######### Directory structure ##########
########################################
	
1. ./AminoAcidChains 							- Contains all the simulation and output data of the MD simulations of amino acid chains
   ./AminoAcidChains/PDB						- Contains PDB files for starting states of each structure
   ./AminoAcidChains/Gromacs					- Contains all files from all parts of the Gromacs MD simulations
   ./AminoAcidChains/analysis					- Contains Python analysis scripts for the MD simulations
   ./AminoAcidChains/results					- Contains processed data and graphs

2. ./BioNetPolymers								- Contains all the simulation andoutput data of the BioNet simulations of globular domain 							  polymers
   ./BioNetPolymers/initialise					- Contains all files required to build the simulation input files for the BioNet simulations
   ./BioNetPolymers/input						- Contains the simulation input files for the BioNet simulations
   ./BioNetPolymers/output						- Contains the raw simulation output files from the BioNet simulations
   ./BioNetPolymers/analysis					- Contains Python analysis scripts for the BioNet simulations
   ./BioNetPolymers/results						- Contains processed data and graphs
   ./BioNetPolymers/movies						- Contains general movies of different types of simulation
   ./BioNetPolymers/movies/SupplementaryMovies	- Contains Supplementary movies of the range of possible flexibilities through the variation 							  of each of our tested material properties and geometric structures

########################################
### Simulation and Analysis Protocol ###
########################################

Dependencies:

	Dependencies for entire simulation and analysis suite. The versions used by us are shown in brackets

	Gromacs (2019.1)
	MDAnalysis (https://www.mdanalysis.org/, 0.19.2)
	Cmake (3.13)
	g++(9.1)
	tinyxml2(https://github.com/leethomason/tinyxml2, master branch)
	Eigen(3.3.7)
	Boost(1.69)
	BioNet(https://bitbucket.org/GokuBH/proteinhydrogelsoftware/branches/, PolyProteinSims branch)

###### Amino acid chain simulations ######

1. Perform appropriately long explicit water MD simulations on the three different amino acid structures:

	cd ./AminoAcidChains/Gromacs
	Proceed through the Gromacs initialisation and simulation routines (http://www.mdtutorials.com/gmx/)

	## Reason - To generate physically realistic flexibility data for a variety of disordered structures

2. Calculate persistence lengths from Gromacs MD trajectories:
	
	cd ./AminoAcidChains/analysis
	python calculatePersistenceLengths.py

	## Reason - To determine flexibility of disoredered proteins and linker domains



###### Globular domain polymer simulations - BioNet Installation ######

1. Download and install BioNet on a Linux machine:

	With an appropriate version of cmake, g++, tinyxml2(http://www.grinninglizard.com/tinyxml2/), Eigen and Boost, execute the commands specified below to install BioNet:

	export BIONETINSTALL=/path/to/install/location
	cd BIONETINSTALL
	mkdir src
	mkdir build
	mkdir install
	cd src
	wget https://bitbucket.org/GokuBH/proteinhydrogelsoftware/get/PolyProteinSims.tar.bz2
	tar -xvf PolyProteinSims.tar.bz2
	cd ../build
	cmake ../src/GokuBH-proteinhydrogelsoftware-6886bde0f9f4/BioNet -DCMAKE_INSTALL_PREFIX=../install -DUSE_OPENMP=NO
	make
	make install
	export PATH=/path/to/install/location/install/bin:$PATH

	export PYTHONPATH=/path/to/install/location/lib/python3.7/site-packages/modules:$PYTHONPATH



###### Globular domain polymer simulation - Free polymers ######

1. Build the set of input scripts for BioNet simulations:

	cd ./BioNetPolymers/initialise
	python buildNMerInputFiles.py

	## Reason - To be able to perform BioNet simulations

2a. Submit the set of input scripts to a supercomputer:

	cd ./BioNetPolymers/initialise
	python buildSubmissionScripts.py
	python submitJobs.py

	## Reason - To quickly perform all required simulations in parallel

				OR

2b. Manually submit the set of input scripts required

	cd ./BioNetPolymers/initialise
	Write a python script to run the jobs. Input (iFname) filenames are of the form:

		iFname=../input/Nodes%d_lOn2R%5.3f_lRFM%5.3f_sE%5.3f.xml

	To run the appropriate BioNet simulation, the command is:

		BioNet-Sim -i iFname -t Brownian --no-vdw --no-kinetics -l --verbose\n"

	This will output files with the correct filenames for further analysis

	## Reason - To generate physically realistic flexibility data for a variety of globular domain polymer systems

3. Calculate persistence lengths for each simulation:

	cd ./BioNetPolymers/analysis
	python calculatePersistenceLengths.py

	## Reason - To determine flexibility of globular domain polymers as a function of their structure and material properties

4. Plot persistence lengths for each simulation:

	cd ./BioNetPolymers/analysis
	python plotPersistenceLengths.py

	## Reason - To visualise the flexibility data of globular domain polymers as a function of their structure and material properties



###### Globular domain polymer simulation - Single Molecule Atomic Force Spectroscopy conditions ######

1. Build the set of input scripts for BioNet simulations:

	cd ./BioNetPolymers/initialise
	python buildForcedNMerInputFiles.py

	## Reason - To be able to perform BioNet simulations

2a. Submit the set of input scripts to a supercomputer:

	cd ./BioNetPolymers/initialise
	python buildForcedSubmissionScripts.py
	python submitForcedJobs.py

	## Reason - To quickly perform all required simulations in parallel

				OR

2b. Manually submit the set of input scripts required

	cd ./BioNetPolymers/initialise
	Write a python script to run the jobs. Input (iFname) filenames are of the form:

		iFname=../input/Nodes%d_lOn2R%5.3fdLOn2R%5.3f_lRFM%5.3f_sE%5.3fForced.xml

	To run the appropriate BioNet simulation, the command is:

		BioNet-Sim -i iFname -t Brownian --no-vdw --no-kinetics -l --verbose\n"

	This will output files with the correct filenames for further analysis

	## Reason - To generate physically realistic flexibility data for a variety of globular domain polymer systems

3. Calculate persistence lengths for each simulation:

	cd ./BioNetPolymers/analysis
	python calculateForceVsExtension.py

	## Reason - To determine flexibility of globular domain polymers under SMFS conditions as a function of their structure and material properties

4. Plot persistence lengths for each simulation:

	cd ./BioNetPolymers/analysis
	python plotForceVsExtension.py
	python plotForceVsExtensionLpLc.py

	## Reason - To visualise the flexibility data of globular domain polymers under SMFS as a function of their structure and material properties