AmberDefaults

object AmberDefaults

Properties

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val chargeMethod: AmberChargeMethod

The default AM1BCC method is currently recommended by Amber for most purposes.

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const val dielectric: Double = 6.0

This appears to be a magic number (for now). Maybe 6 is reasonable for a protein interior?

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const val distanceDependentDielectric: Boolean = true
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const val sqmMinimizationSteps: Int = 0

The default value of 0 assumes the input structure should not be perturbed via minimization. ie, 0 minimization steps results in a single point energy calculation.

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const val vdwScale: Double = 0.95

The default value of 0.95 was determined empirically by early Osprey developers.