Analyses in CPPTRAJ operate on data sets which have been generated by Actions in a prior Run or read in with a readdata command.

Unlike ptraj, Analysis commands in CPPTRAJ do not need to be prefaced with ’analysis’. The exception to this is ’analyze matrix’ in order to differentiate it from the matrix Action command; users are encouraged to use the new command diagmatrix instead.

Like Actions, when an Analysis command is issued it is by default added to the Analysis queue and is not executed until after trajectory processing is completed; a complete list of data sets available for analysis is shown after trajectory processing (prefaced by ’DATASETS’) or can be shown with the ’list dataset’ command. Analyses can also be executed immediately via the runanalysis command.

Note that for Analysis commands that use COORDS data sets, if no COORDS data set is specified then a default one will be automatically created from frames read in by trajin commands.

Command |
Description |
Set Type(s) |

autocorr | Calculate autocorrelation function for multiple data sets. | N 1D scalar |

avg | Calculate average, standard deviation, min, and max for (or over) data sets. | N 1D scalar |

calcstate | Calculate states based on given data sets and criteria. | N 1D scalar |

cluster | Perform cluster analysis. | COORDS, N 1D scalar |

corr, correlationcoe | Calculate auto or cross correlation for 1 or 2 data sets. | 1D scalar, vector |

cphstats | Calculate statistics for constant pH data sets. | pH data sets |

crank, crankshaft | Calculate crankshaft motion between two data sets. | 2 1D scalar |

crdfluct | Calculate atomic fluctuations (RMSF) for atoms over time blocks. | COORDS |

crosscorr | Calculate a matrix of Pearson product-moment N 1D scalar coefficients between given data sets. | N 1D scalar |

curvefit | Perform non-linear curve fitting on given data set. | 1D scalar |

diagmatrix | Calculate eigenvectors and eigenvalues from given symmetric matrix. | symmetric matrix |

divergence | Calculate Kullback-Leibler divergence between two data sets. | 2 1D scalar |

evalplateau | Evaluate whether the data in a 1D set has reached a single exponential plateau. | |

FFT | Perform a fast Fourier transform on data sets. | N 1D scalar |

hausdorff | Calculate the Hausdorff distance for given matrix data set(s). | N 2D matrices |

hist, histogram | Calculate N-dimensional histogram for N given data sets. | N 1D scalar |

integrate | Perform integration on each of the given data sets. | N 1D scalar |

ired | Perform isotropic reoreientational eigenmode dynamics analysis using given IRED vectors. | N IRED vectors |

kde | Calculate 1D histogram from given data set using a kernel density estimator. Also time-dependent Kullback-Leibler divergence analysis with another set. | 1 or 2 1D scalar |

lifetime | Perform lifetime analysis on given data sets. | N 1D scalar |

lowestcurve | For each given data set, calculate a curve that traces the lowest N points over specified bins. | N 1D scalar |

meltcurve | Calculate a melting curve from given data sets assuming simple 2 state kinetics. | N 1D scalar |

modes | Perform various analyses on eigenmodes (from e.g. diagmatrix). | eigenmodes |

multicurve | Perform non-linear curve fitting for multiple input data sets. | N 1D scalar |

multihist | Calculate 1D histograms (optionally with a kernel N 1D scalar density estimator) from multiple input data sets. |
N 1D scalar |

phipsi | Calculate and plot the average phi and psi values from input dihedral data sets. | N phi/psi dihedrals |

regress | Perform linear regression on multiple input data sets. | N 1D scalar |

remlog | Calculate various statistics from a replica log data set. | replica log |

rms2d, 2drms | Calculate 2D RMSD between frames in 1 or 2 COORDS data sets. | 1 or 2 COORDS |

rmsavgcorr | Calculate RMS average correlation curve for a COORDS data set. | COORDS |

rotdif | Calculate rotational diffusion using given rotation matrices (from e.g. rms). | rotation matrices |

runningavg | Calculate running average for given data sets using given window size. | N 1D scalar |

spline | Calculate cubic splines for given data sets. | N 1D scalar |

stat, statistics | Calculate various statistics for given data sets. | N 1D scalar |

ti | Peform Gaussian quadrature integration for given DV/DL data sets. | N 1D scalar |

timecorr | Calculate auto/cross-correlation functions for given vector(s) using spherical harmonics. | 1 or 2 vector |

vectormath | Perform math on given vector data sets. | 2 vectors |

wavelet | Perform wavelet analysis on coordinates from given COORDS set. | COORDS |