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anonymous_namespace{edsam.cpp}::t_edflood Struct Reference
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Description

Essential dynamics flooding parameters and work data. TODO: split into working data and input parameters NOTE: The implementation here follows: O.E. Lange, L.V. Schafer, and H. Grubmuller, “Flooding in GROMACS: Accelerated barrier crossings in molecular dynamics,” J. Comp. Chem., 27 1693–1702 (2006)

Public Attributes

real deltaF0 = 0
 Target destabilisation free energy. Controls the flooding potential strength. Linked to the expected speed-up of mean first passage time out of flooded minimum.
 
bool bConstForce = false
 Do not calculate a flooding potential, instead flood with a constant force.
 
real tau = 0
 Relaxation time scale for slowest flooded degree of freedom.
 
real deltaF = 0
 Current estimated destabilisation free energy.
 
real Efl = 0
 Flooding energy, acting as a proportionality factor for the flooding potential.
 
real kT = 0
 Boltzmann constant times temperature, provided by user.
 
real Vfl = 0
 The flooding potential.
 
real dt = 0
 Integration time step.
 
real constEfl = 0
 Inital flooding strenth.
 
real alpha2 = 0
 Empirical global scaling parameter of the essential dynamics vectors.
 
rvec * forces_cartesian = nullptr
 The forces from flooding in atom coordinate space (in contrast to projections onto essential dynamics vectors)
 
t_eigvec vecs = {}
 The vectors along which to flood.
 
bool bHarmonic = false
 Use flooding for harmonic restraint on the eigenvector.
 
realinitialReferenceProjection = nullptr
 The initial reference projection of the flooding vectors. Only with harmonic restraint.
 
realreferenceProjectionSlope = nullptr
 The current reference projection is the initialReferenceProjection + step * slope. Only with harmonic restraint.
 

The documentation for this struct was generated from the following file: