NonBonding in Pele++ control file

Configuration of the algorithm for non-bonding energy-related terms calculation.

It appears in the “peleSimulation”, “minimization”, “anmComputation”, “sideChainSimulation” commands.

NonBonding v2 algorithm

In this algorithm you only define one cutoff

Example

"NonBonding":
    {
        "nonBondingVersion": "NB_GEN_2",
        "cutoffList":
        [
            {
                "cutoff_v2": 50
            }
        ]
    }

NonBonding multiscale algorithm

This is the default algorithm chosen if you do not include this section in the control file.

In this algorithm we have six different cutoffs. It is the default algorithm for the NonBonding computations.

Example

Example with the default cutoffs.

"NonBonding":
    {
               "nonBondingVersion": "NB_GEN_MSCALE",
               "cutoffList":
               [
                   {
                       "type": "shortNeutrumNeutrum",
                       "value": 10
                   },
                   {
                       "type": "shortChargedNeutrum",
                       "value": 10
                   },
                   {
                       "type": "shortChargedCharged",
                       "value": 15
                   },
                   {
                       "type": "longNeutrumNeutrum",
                       "value": 15
                   },
                   {
                       "type": "longChargedNeutrum",
                       "value": 20
                   },
                   {
                       "type": "longChargedCharged",
                       "value": 30
                   }
               ]
            }