Simulation of a super coarse grained collagen model, that is breakable under force. For details, we refer to the publication
Python version 1.0, contact benedikt.rennekamp@h-its.org for help. Code should be fully usuable, but main purpose of this repository is transparency in reviewing. A clean-up C++ version might become available in the future.
Following parameters can be defined in the main file:
allow_switches: If crosslink would go outside the model, switch direction to retrieve fully crosslink network (default: True)build_up_phase: boolean (default: True)C_path_difference_factor: (default: 1.08) Length of C-terminal path in crosslinked phase compared to standard contourlengthconnectedness: (default: 1.0)constant_force: [N] (default: 3.5e-9)contour_factor: (default: 1.2) Contour length is longer by this factor than initial distancecrosslink_sites: Side of the gap region crosslinks will be made [N,C,BOTH] (default:BOTH)d_phase_arr: Array (default: [1, 4, 3, 2, 0])data_filename: Filename (*.csv) for data (default:data.csv)diffusion_constant: Diffusion constant [m^2/s] (default: 4e-10)dissociation_energy_in_kT: Depth of morse potential [multiple of kT] (default: 119)double_crosslinks: Use this option to double the amount of crosslinks: Connect both up and downwards (default: False)dt: Integration time step [s] (default: 1e-15)dx_max: Maximal integration step size to ensure accurate integration of Smoluchowski equation [m] (default: 1e-10)force_constant_in_kT: Force constant for velocity pulling [multiple of kT] (default: 3.5e18)force_constant_pwWLC: Force constant for enthalpic strechig in piecewise WLC [N/m] (default: 2.05e-8)gap_ratio: (default: 0.54)k_f: [N/m] (default: 440.5 by bondtype C-CT from amber99sb* ffbonded)layers: Only use 1+4*x to get x full repeats of a TH (default: 5)low_up_ratio: Use 1.0 for all crosslinks going to (standard) upper side (default: 1.0)max_extension_percentage: Percentage of fibril length (default: 0.23)N_path_difference_factor: (default: 1.0) Length of N-terminal path in crosslinked phase compared to standard contourlengthpdb_filename: Filename (*.pdb) for trajectory (default:trajectory.pdb)pdb_scaling_factor: (default: 0.01)periodicity: (default: 6.7e-8)persistence_length: [m] (default: 1.45e-8 by Sun et al. 2002 using optical tweezer)plot_freq: Plot only every x-th frame (default: 100)pulltype: [VELOCITY,FORCE,STRAIN] (default:FORCE)r_fb: Flat bottom extra extension of crosslink (default: 1e-9)seed: Random number seed (-1 for random seed) (default: -1)spacing: (default: 1e-8)TH_per_Side: Number of triple helices per side in hexagon (default: 2)time_total: Simulation time [s] (default: 1e-11)tol: Tolerace for identifying equal positions with floats [m] (default: 1e-11)v_pull: [m/s] (default: 25)wlc_functional: [CLASSICAL,PIECEWISE] (deault:PIECEWISE)WLC_max: Cut-off force for WLC to mimick backbone rupture [N] (default: 7.5e-9)write_freq: Write-out frequency in steps (default: 100)