This is part of the colvar module

This Colvar calculates path collective variables.

This is the Path Collective Variables implementation ( see [21] ). This variable computes the progress along a given set of frames that is provided in input ("sss" component) and the distance from them ("zzz" component). (see below).

Warning: The molecule used for PATHMSD calculation should be whole (both atoms used in alignment and in displacement calculation). In case it is broken by the host MD code, please use WHOLEMOLECULES to reconstruct it before PATHMSD calculation.

Description of components

By default this Action calculates the following quantities. These quanties can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.

Quantity	Description
sss	the position on the path
zzz	the distance from the path

Compulsory keywords

LAMBDA	the lambda parameter is needed for smoothing, is in the units of plumed
REFERENCE	the pdb is needed to provide the various milestones

Options

NUMERICAL_DERIVATIVES	( default=off ) calculate the derivatives for these quantities numerically
NEIGH_SIZE	size of the neighbor list
NEIGH_STRIDE	how often the neighbor list needs to be calculated in time units
EPSILON	(default=-1) the maximum distance between the close and the current structure, the positive value turn on the close structure method
LOG-CLOSE	(default=0) value 1 enables logging regarding the close structure
DEBUG-CLOSE	(default=0) value 1 enables extensive debugging info regarding the close structure, the simulation will run much slower
LOG_CLOSE	same as LOG-CLOSE
DEBUG_CLOSE	same as DEBUG-CLOSE

Examples

Here below is a case where you have defined three frames and you want to calculate the progress along the path and the distance from it in p1

p1: PATHMSD REFERENCE=file.pdb  LAMBDA=500.0 NEIGH_STRIDE=4 NEIGH_SIZE=8
PRINT ARG=p1.sss,p1.zzz STRIDE=1 FILE=colvar FMT=%8.4f

note that NEIGH_STRIDE=4 NEIGH_SIZE=8 control the neighborlist parameter (optional but recommended for performance) and states that the neighbor list will be calculated every 4 timesteps and consider only the closest 8 member to the actual md snapshots.

In the REFERENCE PDB file the frames must be separated either using END or ENDMDL.

Note: The implementation of this collective variable and of PROPERTYMAP is shared, as well as most input options.