Simple script for calculating and plotting the order parameter of a molecular system from Desmond Maestro .csv out files after molecular dynamics simulation. Here you can see calculations for molecular system containing separate chromophore molecules with a dipole moment. You can modify it as you wish.
P2 parameter_av - gives you the same graph Maestro can plot right in GUI.
Order_parameter_av - gives you calculated average order parameter for all chromophores during simulation.
Order_parameter_av_reverse_sign_cos3 - taking into account the direction of the chromophore by Cos sign changing (what Desmond program does not take into account).
Please note, that script was written while working on the article [1] for quick assessment of the required values.
[1] Atomistic modeling of electric field poling of PMMA-based polymer material with guest quinoxaline chromophores. Journal of Molecular Liquids 407(5):125224. 2024. DOI:10.1016/j.molliq.2024.125224