private void AddForce(ApproximateAminoAcidForces aminoAcidForces, Vector3D forceDirection, double forceMagnitude)
{
var force = forceMagnitude * forceDirection.To(Unit.Newton);
aminoAcidForces.NitrogenForce += force;
aminoAcidForces.CarbonAlphaForce += force;
aminoAcidForces.CarbonForce += force;
}
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);
}
}
private void RunSimulation(CancellationToken cancellationToken)
{
var simulationTime = simulationSettings.SimulationTime;
var dT = simulationSettings.TimeStep;
for (CurrentTime = 0.To(Unit.Second); CurrentTime < simulationTime; CurrentTime += dT)
{
cancellationToken.ThrowIfCancellationRequested();
var compactnessForces = simulationSettings.UseCompactingForce
? compactnessForceCalculator.Calculate(CompactnessMeasurer.Measure(Peptide))
: new Dictionary <ApproximatedAminoAcid, ApproximateAminoAcidForces>();
var ramachandranForces = simulationSettings.UseRamachandranForce
? ramachandranForceCalculator.Calculate(Peptide)
: new Dictionary <ApproximatedAminoAcid, ApproximateAminoAcidForces>();
var bondForces = bondForceCalculator.Calculate(Peptide);
foreach (var aminoAcid in Peptide.AminoAcids)
{
var resultingForce = new ApproximateAminoAcidForces();
if (compactnessForces.ContainsKey(aminoAcid))
{
var compactnessForce = compactnessForces[aminoAcid];
resultingForce += compactnessForce;
}
if (ramachandranForces.ContainsKey(aminoAcid))
{
var ramachandranForce = ramachandranForces[aminoAcid];
resultingForce += ramachandranForce;
}
if (bondForces.ContainsKey(aminoAcid))
{
var bondForce = bondForces[aminoAcid];
resultingForce += bondForce;
}
ApplyForce(aminoAcid, resultingForce, dT, simulationSettings.ReservoirTemperature);
}
OnSimulationTimestepComplete(new SimulationTimestepCompleteEventArgs(CurrentTime, Peptide));
}
SimulationCompleted?.Invoke(this, EventArgs.Empty);
IsSimulating = false;
}
