SIMONAPreprocessor
GMC Configuration
D_GMC_Config.png
Input files (A)
  • Input configuration: Put the molecule file you want to simulate here.
  • Output xml: Put a name here that you want your output-file to have. The file-extension has to be .xml
  • Parameter file (*.spf): Put the path of a fitting parameter file here. How to create a parameter file is explained here.
Environment (B)
The temperature defines how free to move your molecule is.
  • Constant temperature: Select this to run a simulation with a constant temperature. Enter your temperature in the box beside.
  • Geometric annealing: The temperature of your simulated system will anneal from the start temperature to the end temperature, which have to be entered in the boxes.
Simulation settings (C)
  • Simulation steps: Enter the number of steps here that your simulation should have. This setting is important for the calculation time and result of the simulation.
  • Random seed: Select whether your seed should be random or fixed.
Expert settings (D)
  • How to treat unknown residues: If Fatal is selected the simulation will stop at an unknown residue; If Delete is selected the simulation will proceed anyway. If Ignore is selected, unknown residues issues will be ignored which may cause errors.
  • Set input file format: Usually the input file format is detected automatically. Here you can choose to read in a special file format only.
  • Enable updates and checkpointing: This option allows you to continue crashed simulations.


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