Tools and information for AMBER and CPPTRAJ examples
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
Posted: February 21, 2019
spline <dset0> [<dset1> …] [out <outfile>] [meshsize <n> | meshfactor <x>] [meshmin <mmin>] [meshmax <mmax>] <dsetX> Data set(s) to perform splining on. [out <outfile>] Write splined data to <outfile>. [meshsize<n>] Size of the mesh to use for splining…. Read More
Updated: November 20, 2023
Calculate various statistics for given data sets. stat {<name> | ALL} [shift <value>] [out <filename>] [noeout <filename>] [ignorenv] [name <noe setname>] <name> Name of data set to analyze. ALL analyze all data sets. shift <value> Subtract <value> from… Read More
Updated: March 24, 2019
Peform Gaussian quadrature integration for given DV/DL data sets. <dset0> [<dset1> …] {nq <n quad pts> | xvals <x values>}[name <set name>] [out <file>] [curveout <ti curve file>][nskip <#s to skip>][avgincrement <#> [avgmax <#>] [avgskip <#>]][bs_samples <samples> [bs_points… Read More
Updated: March 24, 2019
Calculate auto/cross-correlation functions for given vector(s) using spherical harmonics. timecorr vec1 <vecname1> [vec2 <vecname2>] out <filename> [order <order>] [tstep <tstep>] [tcorr <tcorr>][dplr] [norm] [drct] [dplrout <dplrfile>] [ptrajformat] vec1 <vecname1> [vec2 <vecname2>] Vector(s) on which to operate. By default the… Read More
Updated: November 20, 2024
Perform math on given vector data sets. vectormath vec1 <vecname1> vec2 <vecname2> [out <filename>] [norm] [name <setname>] [ dotproduct | dotangle | crossproduct | magnitude ] vec1 <vecname1> vec2 <vecname2> Vector(s) on which to operate. [out <filename>] Name… Read More
Updated: March 27, 2019
Perform wavelet analysis on coordinates from given COORDS set. wavelet [crdset <set name>] nb <n scaling vals> [s0 <s0>] [ds <ds>][correction <correction>] [chival <chival>] [type <wavelet>][out <filename>] [name <setname>] [cluster [minpoints <#>] [epsilon <value>] [clusterout <file>] [clustermapout <file>]… Read More
Updated: March 25, 2019
Calculate eigenvectors and eigenvalues from given symmetric matrix. diagmatrix <name> [out <filename>] [thermo [outthermo <filename>]] [vecs <#>] [name <modesname>] [reduce] [nmwiz [nmwizvecs <#>] [nmwizfile <filename>]] <name> Name of symmetric matrix to diagonalize. [out <filename>] Write results to <filename>…. Read More
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