FUNCPATHMSD
 This is part of the function module

This function calculates path collective variables.

This is the Path Collective Variables implementation ( see [9] ). 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 scalar output from one or more other actions. The particular scalars that you will use are referenced using the label of the action. If the label appears on its own then it is assumed that the Action calculates a single scalar value. The value of this scalar is thus used as the input to this new action. If * or *.* appears the scalars calculated by all the proceding actions in the input file are taken. Some actions have multi-component outputs and each component of the output has a specific label. For example a DISTANCE 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.*.More information on the referencing of Actions can be found in the section of the manual on the PLUMED Getting started. Scalar values can also be referenced using POSIX regular expressions as detailed in the section on Regular Expressions. To use this feature you you must compile PLUMED with the appropriate flag. LAMBDA the lambda parameter is needed for smoothing, is in the units of plumed
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
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


In this second example is shown how to define a PATH in the CONTACTMAP space:

CONTACTMAP ...
ATOMS1=1,2 REFERENCE1=0.1
ATOMS2=3,4 REFERENCE2=0.5
ATOMS3=4,5 REFERENCE3=0.25
ATOMS4=5,6 REFERENCE4=0.0
SWITCH=(RATIONAL R_0=1.5)
LABEL=c1
CMDIST
... CONTACTMAP

CONTACTMAP ...
ATOMS1=1,2 REFERENCE1=0.3
ATOMS2=3,4 REFERENCE2=0.9
ATOMS3=4,5 REFERENCE3=0.45
ATOMS4=5,6 REFERENCE4=0.1
SWITCH=(RATIONAL R_0=1.5)
LABEL=c2
CMDIST
... CONTACTMAP

CONTACTMAP ...
ATOMS1=1,2 REFERENCE1=1.0
ATOMS2=3,4 REFERENCE2=1.0
ATOMS3=4,5 REFERENCE3=1.0
ATOMS4=5,6 REFERENCE4=1.0
SWITCH=(RATIONAL R_0=1.5)
LABEL=c3
CMDIST
... CONTACTMAP

p1: FUNCPATHMSD ARG=c1,c2,c3 LAMBDA=500.0
PRINT ARG=c1,c2,c3,p1.s,p1.z STRIDE=1 FILE=colvar FMT=%8.4f