Examples

• TI Calculation
  • Imports
  • Input files
  • Vacuum Simulation
    • Direction A->B
      • Setup:
    • RUN Emin
  • RUN Test SD EQ
  • Further Analysis:
    • Coordinate analysis
    • Energy analysis
  • Lambda Sampling
    • Setup again
  • Submission
  • Free Energy Calculation:
    • TI - Integration Curve
    • Calculate Integration
• Amber2Gromos Example
  • create top + cnf for aniline
  • create top + cnf for aniline, solvated in CHCl3
  • create top + cnf for aniline, solvated in TIP3P water
• Usage of PyGromosTools on HPC-cluster
  • Initialization
  • Energy minimization
    • Print out the new file paths
    • Visualize the minimized system
  • Equilibration followed by subsequent production runs
    • Visualize the last configuration
• QM/MM in Gromos
  • Support for QMMM functionality in GROMOS input files
    • Load an imd file containing a QMMM block
    • Print out different sections of the QMMM block
    • Change a block value and print again
  • Directly manipulate a QMMM specification file
  • Print out and change some blocks in the QMMM specification file
    • Title block
    • QMZONE block
    • QMUNIT block
    • XTBELEMENTS block
    • A helper function that returns all QM engines specified in the QM/MM specification file
    • Store your QMMM specification file with all your other simulation files in a Gromos_System object
  • Run QM/MM Simulations
• Calculation of free energy of evaporization
• OpenFF Automatic Parametrization
• Calculation of Self Solvation Free Energy
  • Do Imports
  • Choose Molecule to run calculation for
    • create the gromos_system from a smile and get the number of atoms
  • Create The Solvation free energy calculation system
    • Create Liquid
    • Minimize Liquid
    • Change the number of cores for longer runs
  • Equilibrate System
  • Do TI calculation
  • Read out results
• 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
      • 1.3) TRC Calculate
      • 1.4) TRC Visualization
    • 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
      • generate coordinates
      • energy minimization - Vacuum
    • Solvatistation and Solvent Energy Minimization
      • build box system
      • 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