private void ApplyForce(ApproximatedAminoAcid aminoAcid,
ApproximateAminoAcidForces resultingForces,
UnitValue timeStepSize,
UnitValue reservoirTemperature)
{
var scaling = 1e0;
var nitrogenForce = scaling * resultingForces.NitrogenForce;
var nitrogenMass = PeriodicTable.GetSingleAtomMass(ElementName.Nitrogen);
var nitrogenAcceleration = nitrogenForce / nitrogenMass;
var nitrogenVelocityChange = nitrogenAcceleration * timeStepSize;
aminoAcid.NitrogenVelocity += nitrogenVelocityChange;
aminoAcid.NitrogenVelocity = InteractWithReservoir(aminoAcid.NitrogenVelocity, nitrogenMass, reservoirTemperature);
aminoAcid.NitrogenPosition += aminoAcid.NitrogenVelocity * timeStepSize;
if (simulationSettings.ResetAtomVelocityAfterEachTimestep)
{
aminoAcid.NitrogenVelocity = new UnitVector3D(Unit.MetersPerSecond, 0, 0, 0);
}
var carbonAlphaForce = scaling * resultingForces.CarbonAlphaForce;
var carbonAlphaMass = PeriodicTable.GetSingleAtomMass(ElementName.Carbon) + AminoAcidSideChainMassLookup.SideChainMasses[aminoAcid.Name];
var carbonAlphaAcceleration = carbonAlphaForce / carbonAlphaMass;
var carbonAlphaVelocityChange = carbonAlphaAcceleration * timeStepSize;
aminoAcid.CarbonAlphaVelocity += carbonAlphaVelocityChange;
aminoAcid.CarbonAlphaVelocity = InteractWithReservoir(aminoAcid.CarbonAlphaVelocity, carbonAlphaMass, reservoirTemperature);
aminoAcid.CarbonAlphaPosition += aminoAcid.CarbonAlphaVelocity * timeStepSize;
if (simulationSettings.ResetAtomVelocityAfterEachTimestep)
{
aminoAcid.CarbonAlphaVelocity = new UnitVector3D(Unit.MetersPerSecond, 0, 0, 0);
}
var carbonForce = scaling * resultingForces.CarbonForce;
var carbonMass = PeriodicTable.GetSingleAtomMass(ElementName.Carbon);
var carbonAcceleration = carbonForce / carbonMass;
var carbonVelocityChange = carbonAcceleration * timeStepSize;
aminoAcid.CarbonVelocity += carbonVelocityChange;
aminoAcid.CarbonVelocity = InteractWithReservoir(aminoAcid.CarbonVelocity, carbonMass, reservoirTemperature);
aminoAcid.CarbonPosition += aminoAcid.CarbonVelocity * timeStepSize;
if (simulationSettings.ResetAtomVelocityAfterEachTimestep)
{
aminoAcid.CarbonVelocity = new UnitVector3D(Unit.MetersPerSecond, 0, 0, 0);
}
}