Tools and information for AMBER and CPPTRAJ examples
Updated: April 6, 2022
Perform various analyses on eigenmodes (from e.g. diagmatrix). modes {fluct|displ|corr|eigenval|trajout|rmsip} name <modesname> [name2 <modesname>] [beg <beg>] [end <end>] [bose] [factor <factor>] [calcall] [out <outfile>] [setname <name>] Options for ’trajout’: (Generate pseudo-trajectory) [trajout <name> parm <name> | parmindex <#>[trajoutfmt… Read More
Updated: March 25, 2019
Perform non-linear curve fitting for multiple input data sets. multicurve set <dset> [set <dset> …]<dset> { <equation> | name <dsname> nexp <m> [form {mexp|mexpk|mexpk_penalty} } [AX=<value> …] [out <outfile>] [resultsout <results>] [maxit <max iterations>] [tol <tolerance>] [outxbins <NX>… Read More
Updated: November 29, 2022
Calculate 1D histograms (optionally with a kernel N 1D scalar density estimator) from multiple input data sets. multihist [out <filename>] [name <dsname>] [norm | normint] [kde] [min <min>] [max <max>] [step <step>] [bins <bins>] [free <T>]<dsetarg0> [ <dsetarg1>… Read More
Updated: March 25, 2019
Calculate and plot the average phi and psi values from input dihedral data sets. phipsi <dsarg0> [<dsarg1> …] resrange <range> [out <file>] <dsargX> Argument selecting data sets. Can specify more than 1. resrange <range> Residue range to use… Read More
Updated: March 25, 2019
Perform linear regression on multiple input data sets. regress <dset0> [<dset1> …] [name <name>] [nx <nxvals>][out <filename>] [statsout <filename>] dsetX Data set(s) to perform linear regression for. name <name> Data set name for resulting linear fits. nx <nxvals>… Read More
Updated: March 25, 2019
Calculate various statistics from a replica log data set. remlog {<remlog dataset> | <remlog filename>} [out <filename>] [crdidx | repidx][stats [statsout <file>] [printtrips] [reptime <file>]] [lifetime <file>] [reptimeslope <n> reptimeslopeout <file>] [acceptout <file>] [name <setname>] <remlog dataset> Previously… Read More
Updated: April 12, 2023
Calculate 2D RMSD between frames in 1 or 2 COORDS data sets. rms2d [crdset <crd set>] [<name>] [<mask>] [out <filename>][dme | nofit | srmsd] [mass][reftraj <traj> [parm <parmname> | parmindex <parm#>] [<refmask>]][corr <corrfilename>] [crdset <crd set>] Name of… Read More
Updated: April 6, 2022
Calculate RMS average correlation curve for a COORDS data set. rmsavgcorr [crdset <crd set>] [<name>] [<mask>] [out <filename>] [mass] [stop <maxwindow>] [offset <offset>] {reference <ref file> parm <parmfile> | first} [crdset <crd set>] COORDS data set to use… Read More
Updated: March 25, 2019
Calculate rotational diffusion using given rotation matrices (from e.g. rms). rotdif [outfile <outfilename>] [usefft] Options for generating random vectors: [nvecs <nvecs>] [rvecin <randvecIn>] [rseed <random seed>] [rvecout <randvecOut>] [rmatrix <set name> [rmout <rmOut>]] Options for calculating vector time… Read More
Posted: February 21, 2019
runningavg <dset1> [<dset2> …] [name <dsetname>] [out <filename>] [ [cumulative] | [window <window>] ] <dset1> [<dset2> …] Data set(s) to calculate running average for. [name <dsetname>] Output running average data set name. [out <filename>] File to write results… Read More
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