FUNCPATHGENERAL

This is part of the function module

This function calculates path collective variables (PCVs) using an arbitrary combination of collective variables.

The method used to calculate the PCVs that is used in this method is described in [52].

This variable computes the progress along a given set of frames that is provided in an input file ("s" component) and the distance from them ("z" component). The input file could be a colvar file generated with plumed driver on a trajectory containing the frames.

The metric for the path collective variables takes the following form:

\[ R[X - X_i] = \sum_{j=1}^M c_j^2 (x_j - x_{i,j})^2\,. \]

Here, the coefficients \(c_j\) determine the relative weights of the collective variables \(c_j\) in the metric. A value for the lambda coefficient also needs to be provided, typically chosen in such a way that it ensures a smooth variation of the "s" component.

Examples

This command calculates the PCVs using the values from the file COLVAR_TRAJ and the provided values for the lambda and the coefficients. Since the columns in the file were not specified, the first one will be ignored (assumed to correspond to the time) and the rest used.

Click on the labels of the actions for more information on what each action computes

path: FUNCPATHGENERAL ...
   
   
LAMBDA
compulsory keyword 
Lambda parameter required for smoothing 
=12.2 
   
REFERENCE
compulsory keyword 
Colvar file needed to provide the CV milestones 
=COLVAR_TRAJ 
   
COEFFICIENTS
compulsory keyword 
Coefficients to be assigned to the CVs 
=0.3536,0.3536,0.3536,0.3536,0.7071 
   
ARG
the input for this action is the scalar output from one or more other actions. 
=d1,d2,d,t,drmsd 
... You cannot view the components that are calculated by each action for this input file. Sorry 

The command below is a variation of the previous one, specifying a subset of the collective variables and using a neighbor list. The columns are zero-indexed. The neighbor list will include the 10 closest frames and will be recalculated every 20 steps.

Click on the labels of the actions for more information on what each action computes

path: FUNCPATHGENERAL ...
   
   
LAMBDA
compulsory keyword 
Lambda parameter required for smoothing 
=5.0 
   
REFERENCE
compulsory keyword 
Colvar file needed to provide the CV milestones 
=COLVAR_TRAJ 
   
COLUMNS
List of columns in the reference colvar file specifying the CVs 
=2,3,4 
   
COEFFICIENTS
compulsory keyword 
Coefficients to be assigned to the CVs 
=0.3536,0.3536,0.3536 
   
ARG
the input for this action is the scalar output from one or more other actions. 
=d2,d,t 
   
NEIGH_SIZE
Size of the neighbor list 
=10 
   
NEIGH_STRIDE
How often the neighbor list needs to be calculated in time units 
=20 
... You cannot view the components that are calculated by each action for this input file. Sorry 

Glossary of keywords and components

Description of components

By default this Action calculates the following quantities. These quantities 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	Position on the path
z	Distance from the path

Compulsory keywords

LAMBDA	Lambda parameter required for smoothing
COEFFICIENTS	Coefficients to be assigned to the CVs
REFERENCE	Colvar file needed to provide the CV milestones

Options

NUMERICAL_DERIVATIVES	( default=off ) calculate the derivatives for these quantities numerically
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 proceeding 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 components 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.. You can use multiple instances of this keyword i.e. ARG1, ARG2, ARG3...
COLUMNS	List of columns in the reference colvar file specifying the CVs
NEIGH_SIZE	Size of the neighbor list
NEIGH_STRIDE	How often the neighbor list needs to be calculated in time units