This function 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 ("s" component) and the distance from them ("z" component). It is a function of MSD that are obtained by the joint use of MSD variable and SQUARED flag (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
s	the position on the path
z	the distance from the path

Compulsory keywords

ARG

the input for this action is the output from one or more other actions. The particular output that you used is referenced using that action of interests label. If the label appears on its own then the value of the relevant Action is taken. If * or *.* appears the information from all arguments is taken. Some actions have multi-component outputs, each component of the output has a specific label so for instance an action labelled dist may have three componets x, y and z. To take just the x component you should use dist.x, if you wish to take all three components then use dist.*

LAMBDA

all compulsory keywords should be added like this with a description here

Options

NUMERICAL_DERIVATIVES

( default=off ) calculate the derivatives for these quantities numerically

NEIGH_SIZE

all optional keywords that have input should be added like a description here

NEIGH_STRIDE

all optional keywords that have input should be added like a description here

Examples

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

t1: RMSD REFERENCE=frame_1.dat TYPE=OPTIMAL SQUARED
t2: RMSD REFERENCE=frame_21.dat TYPE=OPTIMAL SQUARED
t3: RMSD REFERENCE=frame_42.dat TYPE=OPTIMAL SQUARED
p1: FUNCPATHMSD ARG=t1,t2,t3 LAMBDA=500.0
PRINT ARG=t1,t2,t3,p1.s,p1.z STRIDE=1 FILE=colvar FMT=%8.4f