ninnii55/polymer_moleculardynamics

Various bits of code to set up and analyse polymer simulations

Polymer_molecularDynamics

Various bits of code to set up and analyse polymer simulations that were conseptualised in my thesis (Tardiota, N., 2023. Molecular dynamics of gelatin-based peptide systems Doctoral dissertation, Queensland University of Technology).

Polymer_number (Folder) Polymer_number_MD_V1

Directory that contains python code (Polymer_number_MD_V1), whic can be used to calculate how many individual polymers (w/v) and waters are required in a certain simulation box (cube). This currently only calculates the volume (cm^3) of a cubic system. Available in a notbook version (.ipynb) or python file (.py)

Distribution_polymers (Folder)

python code (Polymer_distribution_V1.ipynb) to calcualte PDI of polymer solution in a molecualr dynamic simulation. Also, a number of pokymer generator to generate number of polymers to put in simulation according to (i) Gaussian distribution (ii) high Mw skewed distribution - Stokmeyer, and (iii) Bimodal distribution. This folder also includes associated papers for code inspiration.