Tools and information for AMBER and CPPTRAJ examples
Updated: March 25, 2019
Calculate crankshaft motion between two data sets. crank {angle | distance} <dsetname1> <dsetname2> info <string> [out <filename>] [results <resultsfile>] angle Analyze angle data sets. distance Analyze distance data sets. <dsetname1> Data set to analyze. <dsetname2> Data set to… Read More
Updated: March 25, 2019
Calculate atomic fluctuations (RMSF) for atoms over time blocks. [crdset <crd set>] [<mask>] [out <filename>] [window <size>] [bfactor] Calculate atomic positional fluctuations for atoms in <mask> over windows of size <size>. If bfactor is specified, the fluctuations are… Read More
Updated: March 25, 2019
Calculate a matrix of Pearson product-moment N 1D scalar coefficients between given data sets. crosscorr [name <dsetname>] <dsetarg0> [<dsetarg1> …] [out <filename>] [name <dsetname>] The resulting upper-triangle matrix is stored with name <dsetname>. <dsetarg0> [<dsetarg1> …] Argument(s) specifying… Read More
Updated: March 25, 2019
Perform non-linear curve fitting on given data set. curvefit <dset> { <equation> | name <dsname> { gauss | nexp <m> [form {mexp|mexpk|mexpk_penalty} } } [AX=<value> …] [out <outfile>] [resultsout <results>] [maxit <max iterations>] [tol <tolerance>] [outxbins <NX> outxmin… Read More
Updated: March 25, 2019
Calculate Kullback-Leibler divergence between two data sets. divergence ds1 <ds1> ds2 <ds2> Calculate Kullback-Leibler divergence between specified data sets.
Updated: March 25, 2019
Perform a fast Fourier transform on data sets. fft <dset0> [<dset1> …] [out <outfile>] [name <outsetname>] [dt <samp_int>] <dset0> [<dset1 …] Argument(s) specifying datasets to be used. [out <outfile>] Write results to file named <outfile>. [name <outsetname>] The… Read More
Updated: March 25, 2019
Calculate N-dimensional histogram for N given data sets. hist <dataset_name>[,<min>,<max>,<step>,<bins>] … [free <temperature>] [norm | normint] [gnu] [circular] out <filename> [amd <amdboost_data>] [name <outputset name>] [traj3d <file> [trajfmt <format>] [parmout <file>]] [min <min>] [max <max>] [step <step>] [bins… Read More
Updated: March 25, 2019
Perform integration on each of the given data sets. integrate <dset0> [<dset1> …] [out <outfile>] [name <outsetname>] Integrate specified data set(s) using trapezoid integration.
Updated: March 25, 2019
Perform isotropic reoreientational eigenmode dynamics analysis using given IRED vectors. ired [relax freq <MHz> [NHdist <distnh>]] [order <order>] tstep <tstep> tcorr <tcorr> out <filename> [norm] [drct] modes <modesname> [name <output sets name>] [ds2matrix <file>] [relax freq <MHz> [NHdist <distnh>]]… Read More
Updated: March 25, 2019
Calculate 1D histogram from given data set using a kernel density estimator. Also time-dependent Kullback-Leibler divergence analysis with another set. kde <dataset> [bandwidth <bw>] [out <file>] [name <dsname>][min <min>] [max <max] [step <step>] [bins <bins>] [free] [kldiv <dsname2> [klout… Read More
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