Category: Analysis Commands

autocorr

Calculate autocorrelation function for multiple data sets. autocorr [name <dsetname>] <dsetarg0> [<dsetarg1> …] [out <filename>] [lagmax <lag>] [nocovar] [direct] <dsetarg0> [dsetarg1> …] Argument(s) specifying datasets to be used. [name <dsetname>] Store results in dataset(s) named <dsetname>:X. [out <filename>]… Read More

calcstate

Calculate states based on given data sets and criteria. calcstate {state <ID>,<dataset>,<min>,<max>} [out <state v time file>] [name <setname>] [curveout <curve file>] [stateout <states file>] [transout <transitions file>] state <ID>,<dataset>,<min>,<max> Define a state according to given data set… Read More

cluster

Cluster input frames using the specified clustering algorithm and distance metric. cluster [crdset <crd set> | nocoords] Algorithms: [hieragglo [epsilon ] [clusters ] [linkage|averagelinkage|complete] [epsilonplot ] [includesieved_cdist]] [dbscan minpoints epsilon [sievetoframe] [kdist [kfile ]]] [dpeaks epsilon [noise] [dvdfile… Read More

crank | crankshaft

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

crdfluct

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

crosscorr

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

curvefit

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