Build bicontinuous cubic structure

Follow these steps to build bicontinous cubic structure.

Step 1 : Build initial coarse-grained structure:

• Go to the folder 1_build and source build.sh which runs the python command:
  python build_initial.py -y build.yaml

Step 2: Minimize the initial structure:

• Go to the folder 2_minimize and source the script minimize.sh

Step 3: Solvate with glycerol

• Go to the folder 3_solv_gly and source the script solvate.sh which runs the python command:
  python bcc_solvate.py -y bcc_solvate.yaml

Step 4: Equilibrate

• Go to the folder 4_equilibrate and source the script equilibrate.sh

Step 5: Production run

• Go to the folder 5_prod/T300 and submit the batch job cpu.job

Step 6: Backmap to all-atom model

• Go to the folder 6_backmap/backmapping and submit the batch job backmap.job
  • Note 1: cluster must have Gromacs 2018 installed. The batch job assumes it is installable via module load gromacs/2018
  • Note 2: we provide a yml file with the conda environment needed to run backmapping, so you should ensure you have a working installation of Anaconda3 sourced on your machine

Step 7: Equilibrate the all-atom model

• Go to the folder 7_equil_AA and submit the batch job equil_AA.job

Step 8: Crosslink

• Go to the folder 8_Xlink and source the script run_xlink.sh which runs the python command:
  python bcc_xlink.py -y bcc_xlink.yaml >> bcc_xlink.log

Step 9: Solvate with water

• Go to the folder 9_solv_water and source the script solvate.sh which runs the python command:
  py bcc_solvate.py -y bcc_solvate.yaml

Scripts to replicate our analysis of the pores and transport within the bicontinuous cubic structure.

• MSDF - Minimal surface distribution function
• bilayers - Comparisons between all-atom and CG bilayers
• experimental_pore_size - Parametric bootstrap to get error on experimental pore size estimation
• gyroid_stability - time series of glycerol displacement from the minimal surface, serving as a measure of stability over the simulation
• mathematical_analysis - Mathematical argument to test how bilayers fit within different bicontinuous cubic space groups
• pore_blazer - Pore size distribution over a trajectory performed by PoreBlazer
• transport - Mean square displacement and diffusion coefficient analysis
• visualizations - VMD visualization states of the gyroid structure