Developer Examples

• Implemented pyGromosPP programs
  • Ran_Box
• PyGromos File Examples
  • IMD - Simulation Paramter File
  • CNF - Coordinate File
    • Deleting Residues
    • Generate position Restraint Files
    • Compact all
  • TOP - Topology File
  • TRC - Coordinate Trajectory File
  • Other Files
    • MTB - topology building block file
    • IFP - topology parameter file
    • disres - distance restraint file
  • PTP - Pertubations for free energy calculations
    • defining some state types for later use :)
    • Read in ptp file
    • delete full state
    • delete specific atoms
    • Add atom or state or overwrite atominformation (except atom.NR)
• SD Simulations with Submission System
  • Imports
  • Input files
  • RUN Emin
  • RUN SD Simulation
  • Further Analysis:
    • Coordinate Analysis
    • Energy Analysis
• Gromos Trajectory Examples
  • Example file for the evaluation of GROMOS trajectory files in pygromos
  • 1) TRC
    • 1.1) TRC import
    • 1.2) TRC file handling
      • Save as .h5
    • 1.3) TRC Calculate
    • 1.4) TRC Visualization
      • Do some changes and see how the visualization changes
      • let’s find hydrogenbonds
      • add surface
      • remove surface
      • add transperent cartoon
      • show distance between atom pair
      • once you are happy with the result render and download image
      • Go crazy and make a movie to show off
  • 2) TRE
    • 2.1) Tre import and structure
    • 2.2) Common Tre functions
    • \(\lambda\)-Sampling & TREs
    • EDS in TREs
  • Concatenate and Copy multiple Trajectories
• Gromos Tutorial Pipeline - on a low level
  • Build initial files
    • generate Topology
      • build single topologies
      • combine topology
    • generate coordinates
      • add hydrogens
      • cnf to pdb
    • energy minimization - Vacuum
  • Solvatistation and Solvent Energy Minimization
    • build box system
      • to pdb
    • Add Ions
    • Energy Minimization BOX
  • Simulation
    • Equilibration NVP
    • MD NVP
  • Analysis
• Submission Systems
  • Local Submission
  • LSF Submission
    • Queue Checking:
    • Submission:
    • Submitting multiple jobs
    • Killing a jobs
• Creating and modifying Topologies
  • Automatic System generation and combining of topologies
  • Manual topology modifications