GROMACS mdp files

mdp files to introduce ions (Na, Cl) in the system

  • from Lemkul tutorials, simple as it gets – ions.mdp
    • leonard: /opt/gromacs-2016.1-mod/mdp_files/lemkul_ions.mdp
  • from Rizzo lab, based on a common all-mdp-options template – genion.mdp
    • leonard: /opt/gromacs-2016.1-mod/mdp_files/rizzo_genion.mdp

mdp files for energy minimization (in water)

  • from Lemkul tutorials, lysozime – minim.mdp
    • leonard: /opt/gromacs-2016.1-mod/mdp_files/lemkul_minim.mdp
  • from Rizzo lab, based on a common all-mdp-options template – ubq_min.mdp
    • leonard: /opt/gromacs-2016.1-mod/mdp_files/rizzo_min.mdp

mdp files for NVT equilibration (in water)

  • from Lemkul tutorials, lysozime – nvt.mdp
    • leonard: /opt/gromacs-2016.1-mod/mdp_files/lemkul_nvt.mdp
  • from Rizzo lab, based on a common all-mdp-options template – ubq_nvt.mdp
    • leonard: /opt/gromacs-2016.1-mod/mdp_files/rizzo_nvt.mdp