OpenMM
|
DualAMDIntegrator implements a dual boost aMD integration algorithm. More...
Public Member Functions | |
def | __init__ |
Create a DualAMDIntegrator. More... | |
def | getAlphaTotal |
Get the value of alpha for the total energy. More... | |
def | setAlphaTotal |
Set the value of alpha for the total energy. More... | |
def | getETotal |
Get the energy threshold E for the total energy. More... | |
def | setETotal |
Set the energy threshold E for the total energy. More... | |
def | getAlphaGroup |
Get the value of alpha for the boosted force group. More... | |
def | setAlphaGroup |
Set the value of alpha for the boosted force group. More... | |
def | getEGroup |
Get the energy threshold E for the boosted force group. More... | |
def | setEGroup |
Set the energy threshold E for the boosted force group. More... | |
def | getEffectiveEnergy |
Given the actual potential energy of the system, return the value of the effective potential. More... | |
DualAMDIntegrator implements a dual boost aMD integration algorithm.
This is similar to AMDIntegrator, but two different boosts are applied to the potential: one based on the total energy, and one based on the energy of a single force group (typically representing torsions).
For details, see Hamelberg et al., J. Chem. Phys. 127, 155102 (2007).
def __init__ | ( | self, | |
dt, | |||
group, | |||
alphaTotal, | |||
ETotal, | |||
alphaGroup, | |||
EGroup | |||
) |
Create a DualAMDIntegrator.
dt | (time) The integration time step to use |
group | (int) The force group to apply the second boost to |
alphaTotal | (energy) The alpha parameter to use for the total energy |
ETotal | (energy) The energy cutoff to use for the total energy |
alphaGroup | (energy) The alpha parameter to use for the boosted force group |
EGroup | (energy) The energy cutoff to use for the boosted force group |
References CustomIntegrator.addComputeGlobal(), CustomIntegrator.addComputePerDof(), CustomIntegrator.addConstrainPositions(), CustomIntegrator.addGlobalVariable(), CustomIntegrator.addPerDofVariable(), and CustomIntegrator.addUpdateContextState().
def getAlphaGroup | ( | self | ) |
Get the value of alpha for the boosted force group.
References CustomIntegrator.getGlobalVariable().
Referenced by DualAMDIntegrator.getEffectiveEnergy().
def getAlphaTotal | ( | self | ) |
Get the value of alpha for the total energy.
References CustomIntegrator.getGlobalVariable().
Referenced by DualAMDIntegrator.getEffectiveEnergy().
def getEffectiveEnergy | ( | self, | |
totalEnergy, | |||
groupEnergy | |||
) |
Given the actual potential energy of the system, return the value of the effective potential.
totalEnergy | (energy): the actual potential energy of the whole system |
groupEnergy | (energy): the actual potential energy of the boosted force group |
References AMDForceGroupIntegrator.getAlphaGroup(), DualAMDIntegrator.getAlphaGroup(), DualAMDIntegrator.getAlphaTotal(), AMDForceGroupIntegrator.getEGroup(), DualAMDIntegrator.getEGroup(), and DualAMDIntegrator.getETotal().
def getEGroup | ( | self | ) |
Get the energy threshold E for the boosted force group.
References CustomIntegrator.getGlobalVariable().
Referenced by DualAMDIntegrator.getEffectiveEnergy().
def getETotal | ( | self | ) |
Get the energy threshold E for the total energy.
References CustomIntegrator.getGlobalVariable().
Referenced by DualAMDIntegrator.getEffectiveEnergy().
def setAlphaGroup | ( | self, | |
alpha | |||
) |
Set the value of alpha for the boosted force group.
References CustomIntegrator.setGlobalVariable().
def setAlphaTotal | ( | self, | |
alpha | |||
) |
Set the value of alpha for the total energy.
References CustomIntegrator.setGlobalVariable().
def setEGroup | ( | self, | |
E | |||
) |
Set the energy threshold E for the boosted force group.
References CustomIntegrator.setGlobalVariable().
def setETotal | ( | self, | |
E | |||
) |
Set the energy threshold E for the total energy.
References CustomIntegrator.setGlobalVariable().