Action: FUNCPATHGENERAL

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

Output components

This action calculates the values in the following table. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.

Input

The arguments that serve as the input for this action are specified using one or more of the keywords in the following table.

Further details and examples

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 the paper from the bibliography below.

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

FUNCPATHGENERALThis function calculates path collective variables (PCVs) using an arbitrary combination of collective variables. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=path
LAMBDALambda parameter required for smoothing=12.2
REFERENCEColvar file needed to provide the CV milestones=COLVAR_TRAJ
COEFFICIENTSCoefficients to be assigned to the CVs=0.3536,0.3536,0.3536,0.3536,0.7071
ARGthe labels of the values from which the function is calculated=d1,d2,d,t,drmsd
... FUNCPATHGENERAL
The FUNCPATHGENERAL action with label path calculates the following quantities:
 Quantity   
 Description  
path.s
Position on the path
path.z
Distance from the path

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

FUNCPATHGENERALThis function calculates path collective variables (PCVs) using an arbitrary combination of collective variables. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=path
LAMBDALambda parameter required for smoothing=5.0
REFERENCEColvar file needed to provide the CV milestones=COLVAR_TRAJ
COLUMNSList of columns in the reference colvar file specifying the CVs=2,3,4
COEFFICIENTSCoefficients to be assigned to the CVs=0.3536,0.3536,0.3536
ARGthe labels of the values from which the function is calculated=d2,d,t
NEIGH_SIZESize of the neighbor list=10
NEIGH_STRIDEHow often the neighbor list needs to be calculated in time units=20
... FUNCPATHGENERAL
The FUNCPATHGENERAL action with label path calculates the following quantities:
 Quantity   
 Description  
path.s
Position on the path
path.z
Distance from the path

References

More information about how this action can be used is available in the following articles: - L. Hovan, F. Comitani, F. L. Gervasio, Defining an Optimal Metric for the Path Collective Variables. Journal of Chemical Theory and Computation. 15, 25–32 (2018)

Syntax

The following table describes the keywords and options that can be used with this action