HISTOGRAM

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

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