Commands block in PELE++

A simulation is made up of a set of different commands. Once they all finish, the simulation also finishes.

Commands description

Array containing the list of all the commands.

commandType

Every command must contain this field. We can launch different kinds of command:

• “peleSimulation”: Most important block. It performs a Pele simulation.

• “energyComputation”: Performs an energy computation.

• “minimization”: Performs a minimization.

• “anmComputation”: Performs an ANM computation.

• “sideChainSimulation”: Performs a Side Chain Prediction simulation.

Example 1

Energy computation:

{
   "controlFileSavingPath" : "../../simulations/ain/originalControlFile.conf",
   "Initialization" : {
      "Complex" : {
         "files" : [
            {
               "path": "../proteins/ain_fixed.pdb"
            }
         ]
      },
      "ForceField" : "OPLS2005",
      "Solvent" : {
         "ionicStrength" : 0.250,
         "solventType" : "VDGBNP",
         "useDebyeLength" : true
      }
   },
   "commands" : [
      {
       "commandType":"energyComputation"
      }
   ]
}

Example 2

We can link together different commands. For example, we can minimize the structure before running a Pele simulation.

{
    ...
    "commands": [
        {
            "commandType": "minimization",
            "Minimizer":
            {
                "algorithm": "TruncatedNewton",
                "parameters":
                {
                    "MinimumRMS": 0.05
                }
            }
        },
        {
            "commandType": "peleSimulation",
            ...
        }
    ]
}