Tools and information for AMBER and CPPTRAJ examples
Updated: November 20, 2024
Project data along eigenmodes projectdata evecs <evecs dataset> [name <name>] [out <outfile>] [beg <beg>] [end <end>]{[dihedrals <dataset arg>] | [data <dataset arg> …]} evecs <dataset name> Data set containing eigenvectors (modes). [name <name>] Output data set name. [out… Read More
Category: Analysis Commands, CPPTRAJ
Updated: November 20, 2024
Perform time-independent correlation analysis (TICA) tica { crdset <COORDS set name> [mask <mask>] | data <input set arg1> … } [lag <time lag>] [map {kinetic | commute | none}] [name… Read More
Category: Analysis Commands, CPPTRAJ
Updated: April 6, 2022
Calculate statistics for constant pH data sets. cphstats <pH sets> [name <name>] [statsout <statsfile>] [deprot] [fracplot [fracplotout <file>]] <pH sets> Previously read in pH data sets. name <name> Output set name. statsout <statsle> Write pH statistics to <statsfile>… Read More
Category: Analysis Commands, CPPTRAJ
Updated: March 25, 2019
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
Updated: October 16, 2024
Calculate average, standard deviation, min, and max for (or over) data sets. Not to be confused with the average command. avg <dset0> [<dset1> …] [torsion] [out <file>] [oversets] [name <name>] [nostdout] <dsetX> Data set(s) to calculate the average… Read More
Updated: March 30, 2019
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
Updated: July 1, 2023
Cluster input frames using the specified clustering algorithm and distance metric. cluster [crdset <crd set>] [data <dset0> [,<dset1>…]] [nocoords] [<name>] [<Algorithm>] [<Metric>] [<Pairwise>] … Read More
Updated: March 25, 2019
Calculate auto or cross correlation for 1 or 2 data sets. corr out <outfilename> <dataset1> [<dataset2>] [lagmax <lag>] [nocovar] [direct] out <outfilename> Write results to file named <outfilename>. The datasets must have the same # of data points…. Read More
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
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