Calculate the probability density as a function of a few CVs using kernel density estimation

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.*
STRIDE	( default=1 ) the frequency with which data should be stored for analysis
RUN	the frequency with which to run the analysis algorithm. This is not required if you specify USE_ALL_DATA
GRID_MIN	the lower bounds for the grid
GRID_MAX	the upper bounds for the grid
GRID_BIN	the number of bins for the grid
KERNEL	( default=gaussian ) the kernel function you are using. More details on the kernels available in plumed can be found in kernelfunctions.
BANDWIDTH	the bandwdith for kernel density estimation
GRID_WFILE	( default=histogram ) the file on which to write the grid

Options

USE_ALL_DATA	( default=off ) use the data from the entire trajectory to perform the analysis
REWEIGHT_BIAS	( default=off ) reweight the data using all the biases acting on the dynamics. For more information see reweighting.
WRITE_CHECKPOINT	( default=off ) write out a checkpoint so that the analysis can be restarted in a later run
NOMEMORY	( default=off ) analyse each block of data separately

FMT

the format that should be used in analysis output files

TEMP

the system temperature. This is required if you are reweighting.

REWEIGHT_TEMP

reweight data from a trajectory at one temperature and output the probability distribution at a second temperature. For more information see reweighting. This is not possible during postprocessing.

Examples

The following input monitors two torsional angles during a simulation and outputs a histogram as a function of them at the end of the simulation.

TORSION ATOMS=1,2,3,4 LABEL=r1
TORSION ATOMS=2,3,4,5 LABEL=r2
HISTOGRAM ...
ARG=r1,r2
USE_ALL_DATA
GRID_MIN=-3.14,-3.14
GRID_MAX=3.14,3.14
GRID_BIN=200,200
BANDWIDTH=0.05,0.05
GRID_WFILE=histo
... HISTOGRAM

The following input monitors two torsional angles during a simulation and outputs the histogram accumulated thus far every 100000 steps.

TORSION ATOMS=1,2,3,4 LABEL=r1
TORSION ATOMS=2,3,4,5 LABEL=r2
HISTOGRAM ...
ARG=r1,r2
RUN=100000
GRID_MIN=-3.14,-3.14
GRID_MAX=3.14,3.14
GRID_BIN=200,200
BANDWIDTH=0.05,0.05
GRID_WFILE=histo
... HISTOGRAM

The following input monitors two torsional angles during a simulation and outputs a separate histogram for each 100000 steps worth of trajectory.

TORSION ATOMS=1,2,3,4 LABEL=r1
TORSION ATOMS=2,3,4,5 LABEL=r2
HISTOGRAM ...
ARG=r1,r2
RUN=100000 NOMEMORY
GRID_MIN=-3.14,-3.14
GRID_MAX=3.14,3.14
GRID_BIN=200,200
BANDWIDTH=0.05,0.05
GRID_WFILE=histo
... HISTOGRAM