- Input file (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
- 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)
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- 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.
- Set input file format: Usually the input file format is detected automatically. Here you can choose to read in a special file format only.
- Remove apolar atoms: Removes apolar atmos.
- Enable updates and checkpointing: This option allows you to continue crashed simulations. .