Input files for DPD simulations: initial configurations and parameter script

------------------------------------------------------------ SOFTWARE REQUIREMENTS ------------------------------------------------------------ - GALAMOST 4.0.2 (DPD simulation packages) URL: [pygamd.com/] - Python 3.11 with the following packages: - numpy - pandas - Bash shell (for running .sh scripts) ------------------------------------------------------------ DPD SIMULATION INPUT FILES For: Polymer cyclization on patterned surfaces ============================================================ This dataset contains the initial configuration generation files, DPD simulation parameter scripts used to produce the data reported in the study. 1. submit_all_dpd_sims.sh - Main submission script for all DPD simulations. - Executes the complete workflow in the correct order. 2. gen_free_chain.molg - Generates the initial configuration of a free polymer chain in the solution. 3. gen_patterned_surface.py - Python script that generates the patterned surface with hexagonally arranged circular adsorptive patterns. 4. gen_wall.molg - Generates a dense particle configuration from which the wall will be extracted (subtracted) in subsequent steps. 5. merge_chain_surface.molg - Merges the free chain with the patterned surface, generating the complete initial configuration. 6. set_reactive_ends.py - Sets the chain ends as reactive (activates reactivity) for cyclization studies. 7. move_chain.py - Adjusts the position of the chain relative to the patterned surface prior to simulation. 8. relax_solvent.gala - Input parameter file for solvent relaxation prior to the cyclization simulation. 9. equi_free_chain.gala - Input file for equilibrating the free chain in solution. 10.

Density_plate_adsorption.py - Python script for analyzing the adsorption fraction of chains on the patterned surface. 11. cyclization.gala - Main DPD input file for the cyclization simulation.