This Colvar calculates path collective variables.

This is the Path Collective Variables implementation ( see [3] ). 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).

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

NOPBC

( default=off ) ignore the periodic boundary conditions when calculating distances

NEIGH_SIZE

size of the neighbor list

NEIGH_STRIDE

how often the neighbor list needs to be calculated in time units

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.

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