gmx::DensityFittingParameters Struct Reference

#include <gromacs/applied_forces/densityfitting/densityfittingparameters.h>

Description

Holding all directly user-provided parameters for density fitting.

Also used for setting all default parameters.

Public Attributes
bool	active_ = false
	Indicate if density fitting is active.
std::vector< Index >	indices_
	Indices of the atoms that shall be fit to the density.
DensitySimilarityMeasureMethod	similarityMeasureMethod_ = DensitySimilarityMeasureMethod::innerProduct
	Determines how to measure similarity between simulated and reference density.
DensityFittingAmplitudeMethod	amplitudeLookupMethod_ = DensityFittingAmplitudeMethod::Unity
	Determines with what weight atoms are spread.
real	forceConstant_ = 1e9
	The force constant to be used for the density fitting.
real	gaussianTransformSpreadingWidth_ = 0.2
	The spreading width used for the gauss transform of atoms onto the density grid.
real	gaussianTransformSpreadingRangeInMultiplesOfWidth_ = 4.0
	The spreading range for spreading atoms onto the grid in multiples of the spreading width.
std::int64_t	calculationIntervalInSteps_ = 1
	Apply density fitting forces only every n-steps.
bool	normalizeDensities_ = true
	Normalize reference and simulated densities.
bool	adaptiveForceScaling_ = false
	Perform adaptive force scaling during the simulation.
real	adaptiveForceScalingTimeConstant_ = 4
	The time constant for the adaptive force scaling in ps.
std::string	translationString_
	Translation of the structure, so that the coordinates that are fitted are x+translation.
std::string	transformationMatrixString_
	Linear transformation of the structure, so that the coordinates that are fitted are Matrix * x.

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

• src/gromacs/applied_forces/densityfitting/densityfittingparameters.h