Tag: analysis


Project coordinates along given eigenvectors. projection [<name>] evecs <dataset name> [out <outfile>] [beg <beg>] [end <end>] [<mask>] [dihedrals <dataset arg>] [start <start>] [stop <stop>] [offset <offset>] [<name>] Output data set name. evecs <dataset name> Data set containing eigenvectors… Read More


Calculate secondary structure content using the DSSP algorithm secstruct [<name>] [out <filename>] [<mask>] [sumout <filename>][assignout <filename>] [totalout <filename> [ptrajformat] [namen <N name>] [nameh <H name>] [nameca <CA name>][namec <C name>] [nameo <O name>] [<name>] Output data set name…. Read More


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


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 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