Analysis Commands

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  Calculate auto or cross correlation for 1 or 2 data sets.  1D scalar, vector
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
FFT Perform a fast Fourier transform on data sets. N 1D scalar
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