SKETCHMAP_PROJECTION

	This is part of the dimred module
	It is only available if you configure PLUMED with ./configure –enable-modules=dimred . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list.

Read in a sketch-map projection

Examples

Glossary of keywords and components

Description of components

Quantity	Keyword	Description
gspath	GPATH	the position along the path calculated using the geometric formula
gzpath	GPATH	the distance from the path calculated using the geometric formula
spath	GPATH	the position along the path calculated using the geometric formula
zpath	GPATH	the distance from the path calculated using the geometric formula

Compulsory keywords

REFERENCE	a pdb file containing the set of reference configurations
TYPE	( default=OPTIMAL-FAST ) the manner in which distances are calculated. More information on the different metrics that are available in PLUMED can be found in the section of the manual on Distances from reference configurations
PROPERTY	the property to be used in the index. This should be in the REMARK of the reference
WEIGHT	the weight of each individual landmark in the stress fucntion that is to be optimised
HIGH_DIM_FUNCTION	the parameters of the switching function in the high dimensional space
LOW_DIM_FUNCTION	the parameters of the switching function in the low dimensional space
CGTOL	( default=1E-6 ) The tolerance for the conjugate gradient minimization that finds the out of sample projections

Options

NOPBC	( default=off ) ignore the periodic boundary conditions when calculating distances
NOSPATH	( default=off ) do not calculate the spath CV
NOZPATH	( default=off ) do not calculate the zpath CV
GPATH	( default=off ) calculate the trigonometric path
ARG	the list of arguments you would like to use in your definition of the path
COEFFICIENTS	the coefficients of the displacements along each argument that should be used when calculating the euclidean distance