Gromos related commands (GROMOS)

• Introduction.
• Setting up GROMOS for use with WHAT IF:
• Automatic options
  • Automatic EM (FASTEM)
  • Automatic MD (FASTHT)
  • Automatic MD (FASTMD)
• Making GROMOS files for small molecules
  • Introduction
  • Gromos preprocessor for small molecules with DAVADRUG
• Energy per atom (GETETM)
• Graphical energy output ETPLOT
• Gromos pre-processor
  • Introduction
  • Creating topology file (WREGRO)
  • Energy minimization (WRUNEM)
  • Molecular dynamics (HEATUP)
  • Molecular dynamics (WRUNMD)
  • Molecular dynamics continuation (CONTMD)
• Fixing alpha carbons during a em or md run
• Looking at output
  • Look at progmt output (SHOGMT)
  • Look at progch output (SHOGCH)
  • Look at progwh output (SHOGWH)
  • Look at proem output (SHOEM)
  • Look at promd output (SHOMD)
  • Look at prommt output (SHOMMT)
  • Look at probox output (SHOBOX)
  • Look at proion output (SHOION)
  • Manual editing of GROMOS topology (EDITOP)
  • Viewing energy files from an MD run (ENERAN)
  • Write a GROMOS coordinate file (MAKGRO)
  • Merge two binary topologies (MRGTOP)
• Parameters for wre-gromos
  • Parameters for GROMOS (PARAMS)
    • (LEVUSE)
    • Type of EM (MINTYP)
    • Type of MD startup (MDINIT)
    • EM nr. of steps (STEPS)
    • Gradient correction (NEWGRD)
    • SHAKE usage (ISHAKE)
    • (MINDIF)
    • (STPSIZ)
    • EM step size (MAXSTP)
    • Output format (XTCASC)
    • Positioning of hydrogens (HPLACE)
    • Fix alpha carbon positions (FIXCAS)
    • Fixing force (FIXFRC)
    • Steps in startup (HTSTEP)
    • Steps in MD (MDSTEP)
    • (TEMP)
    • (RCUTP)
    • (RCUTL)
    • (TEMPER)
    • (TRAJEC)
    • (TRASTP)
• Special features
  • Creating torsion angle restraint input cards (TRSFIL)
• Limitations
• Using GROMACS (PREGMX)
  • Makes a GROMACS coordinate file and binary topology file (MAKTPB)
  • Same as MAKTPB, but including solvent/ions (MAKBOX)
  • Same as MAKBOX + energy minimisation of the system (GMXFEM)
  • Same as GMXFEM + position restrained MD (startup) run (GMXFPR)
  • Same as GMXFPR + continuation MD run (GMXFMD)
  • Parameters for (GMXPAR)
    • The short range cut-off radius (CUTOF1)
    • The long range cut-off radius (CUTOF2)
    • Number of steps in energy minimisation (EMSTPS)
    • Number of steps in startup of position restrained MD (PRSTPS)
    • Number of steps in continuation MD (MDSTPS)
    • Frequency of writing various properties to output file (WRTFRQ)
    • Frequency of writing trajectory frames to XTC file (XTCFRQ)
    • Flag to select whether remote waters should be removed (DELH2O)
    • Minimum distance from protein to any edge of box (BOXDIS)
    • Level of interaction (INTLEV)
    • Position restraints (FIXPAR)
    • Position restraining force (FIXFGM)
    • Distance restraning parameters (RESUSE)
    • Box type used (BOXLEV)