Collaboration diagram for anonymous_namespace{edsam.cpp}::t_edflood:

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.

real *	initialReferenceProjection = nullptr
	The initial reference projection of the flooding vectors. Only with harmonic restraint.

real *	referenceProjectionSlope = 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:

src/gromacs/essentialdynamics/edsam.cpp

Description

Public Attributes