Gromos related commands (GROMOS)

• Introduction.
• Setting up GROMOS for use with WHAT IF:
• Automatic options (READ THIS IF YOU WANT TO USE EM/MD WITHOUT GETTING INTO DETAILS) (FASTXX)
• Project number (PROJEC)
• Making GROMOS files for small molecules
  • Introduction
  • Gromos preprocessor for small molecules (DAVADRUG)
• Energy per atom (GETETM)
• Graphical energy output (ETPLOT)
• Gromos pre-processor
  • Introduction
  • Creating topology file (WREGRO)
  • Energy minimization (WRUNEM)
  • Molecular dynamics (HEATUP/WRUNMD)
  • Molecular dynamics continuation (MDCONT)
• Fixing alpha carbons during a em or md run
• Looking at output
  • Look at progmt output (SHOGMT)
  • Look at progmt output (SHOGM2)
  • Look at progch output (SHOGCH)
  • Look at progwh output (SHOGCH)
  • Look at proem output (SHO-EM)
  • Look at promd output (SHO-MD)
  • Look at prommt output (SHOMMT)
  • Look at probox output (SHOBOX)
  • Look at proion output (SHOION)
• Parameters for wre-gromos
  • Parameters for GROMOS (PARAMS)
  • Parameters for adding waters (PARBOX)
• Special features
  • Checking coordinates and nomenclature (GCHECK)
  • Creating torsion angle restraint input cards
• Limitations