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MolDynamics_gromacs

  • MDP_files
    • Atomistic MD simulation (ATMD) parameters for EM, EQ, PROD - CHARMM36(m) ff
    • Coarse-gr MD simulation (CGMD) parameters for EM, EQ, PROD - MARTINI 2.2 ff
  • Analysis
    • do-order-multi_feb2023.py - script to calc lipid order param for Martini 2 lipids
    • count_num_of_lip-sol_in_gro_file.sh - script to quickly calc and print num of lipids and solvent molecules in a GRO file.
    • pylipid_residence_time_analysis_r1-3 - directory containing a zip file with scripts and empty dirs ready for residence time analysis.
  • dssp
    • contains a dssp executable and a deb file.