Tutorials

• Gromos Tutorial
  • Build the input files
    • The Topology File
      • Building the Topology File
    • The Coordinate File
      • Periodic Boxes
      • Building the Coordinate File
      • add hydrogens
      • Optional: Convert cnf to pdb
    • Energy Minimization - Vacuum
      • Simulation Parameter File
      • Perform Emin
      • Analysis
  • Solvatistation and Solvent Energy Minimization
    • build box system
    • Add Ions
    • Energy Minimization BOX
      • build posistion restraints
      • Perform Emin
  • Thermalisation and equilibration.
    • Simulation Paramters
      • Initialise Block
    • System Block
      • STEP Block
      • BOUNDCOND Block
      • MULTIBATH Block
    • COMTRANSROT Block
    • COVALENTFORM Block
    • WRITETRAJ Block
    • PRINTOUT Block
    • PAIRLIST Block
    • POSITIONRES Block
    • Perform Thermalisation
    • Analysis of Thermalisation:
      • Check the coordinate traj
      • Check the temperature
  • Molecular dynamics sampling simulation.
    • Simulation Paramters
    • Perform MD - Production
    • Analysis
      • First Look Analysis
      • Energy Analysis
      • Coordinate Analysis
      • Distance CL- to the peptide