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Daniel R. Roe edited this page Mar 15, 2016 · 15 revisions
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Welcome to the CPPTRAJ wiki!

Here you will find (hopefully) useful information on using and developing CPPTRAJ.

New In CPPTRAJ

Warning: This functionality by and large pertains to the development version of CPPTRAJ and should be used with caution.


As of March 15, 2016

File Formats

  • Charmm COR (read only)
  • Gromacs XVG (read only)
  • Gromacs TOP (read only)
  • CCP4 Grid Density (read/write)
  • PDB files:
    • Read and write more information (insertion codes, chain IDs, CRYST1, CONECT records, etc).
    • Improved element determination.
  • OpenDX files
    • bincenter: On write grid mesh can be aligned on grid bin centers instead of corners.
    • gridwrap: Like bincenter but also wrap grid density.
    • gridext: Like bincenter but also print an extra layer of empty bins.
  • NetCDF trajectory files: Can now read/write force information.
  • Mol2 files: sybyltype: Can output SYBYL atom types in Mol2 files if AMBERHOME is set.
  • Add keepext keyword to the amber restart, ncrestart, mol2, and pdb file formats to keep the extension intact and prepend the set number to the extension instead (e.g. out.X.pdb).

General

  • Across trajectory parallelization with cpptraj.MPI. Input trajectory/ensemble reads/writes are now parallelized in cpptraj.MPI.
    • New command ensemblesize should be used with cpptraj.MPI to improve efficiency of ensemble set up in parallel.
  • Data files can be converted via command line, e.g. cpptraj -d input.dat -w output.agr
  • onlymembers <list> keyword for trajout/outtraj; during ensemble run only write trajectory data for specified ensemble members.
  • Simple math can be performed with 2D/3D (matrix/grid) data sets (addition, subtraction, etc).
  • Can be configured with both MPI and OpenMP at the same time.
  • Non-data set file output from most Actions (e.g. hbond avgout) can be combined.
  • rotdif is now an Analysis.
  • Will now compile under Windows.
  • dataset
    • Data sets can be concatenated with dataset cat <dataset> <dataset> ...
    • Can create new data set with X values from one set and Y values from another: dataset makexy <set1> <set2>
  • Can manipulate reference structures using crdaction, so e.g. reference coordinates can be stripped, translated, rotated, etc.
  • Can be compiled without ARPACK (makes diagmatrix with larger matrices very slow).
  • Compressed (gzip/bzip2) input files can be read.
  • dihedralscan has been renamed permutedihedrals to better reflect what the command does.

Actions

  • esander: Calculate energies from sander (PME/GB) if compiled with sander API.
  • diffusion
    • Now uses data set framework, can control of output format/precision etc.
    • New syntax, average is the default (old syntax still supported):
diffusion
        [{out <filename> | separateout <suffix>}] [time <time per frame>]
        [<mask>] [<set name>] [individual] [diffout <filename>] [nocalc]
* Automatically calculate diffusion constants from linear regression.
* Fix orthothombic imaging bug.
* Support non-orthorhombic imaging; faster than having a preceding **unwrap**.
  • New keyword parmout <top file> added to closest and strip commands for writing out topology files.
  • nastruct
    • Base pairing detection improved. Can detect non-WC base pairing, and base pairs in multi-stranded systems (e.g. G-quadruplex.
    • Better handling of systems where base pairs break and reform.
    • allframes: Recalculate base pairing each frame.
    • groovecalc: Can now specify 3dna to perform groove calculation of El Hassan and Calladine (as opposed to simple which is just based on phosphate/O4' distances).
    • New output column for BP.<suffix> file: BP, set to 1 if base pair present and 0 otherwise.
    • calcnohb: If specified base pair parameters will be calculated even if no hydrogen bonds present between previously found base pair.
  • closest: center option added for using center of mass of solute (instead of all atoms).
  • symmrmsd: Speedup; fixed bug in Hungarian algorithm that caused slow convergence.
  • rms
    • savematrices: Save rotation matrices to data set <name>[RM]
    • nomod keyword to prevent modification of coords even when calculating best-fit RMSD.
  • rotate
    • Can rotate around axis created from two points defined by user: axis0 <mask0> axis1 <mask1>.
    • Can rotate from rotation matrices data set (from e.g. rms savematrices): usedata <set name> [inverse]
  • replicatecell: Can now replicate more than 1 image in any direction.

Analysis

  • vectormath: Can perform calculations on two vectors each of size N, or one vector of size 1 and another vector of size N.
  • ti: Calculate average DV/DL from input data sets and perform Gaussian quadrature integration.
  • modes: Fix fluct and displ for when eigenvalues are not in units of cm^-1. Also add option calcall to not skip zero/negative eigenvectors.
  • curvefit: Add gauss keyword to fit Gaussian.

As of September 24, 2015

File Formats

  • Gromacs GRO (read only)

General

  • Ability to read and process constant pH REMD logs.
  • PDB files:
    • CONECT records used to determine bonds; also add noconect option to PDB parm read to prevent using CONECT records to determine bonds.
    • For PDB write, add include_ep keyword to enable write of extra points.
  • Fix segfault when using DataSet_Coords_TRJ with trajectories containing velocity information.
  • Fix reading MDOUT from pememd TI run.
  • Fix residue single char output (TYR mistakenly converted to R instead of Y).
  • Data sets should now be properly appended to by readdata.
  • Can be configured to use FFTW3 (configure -fftw3 --with-fftw3=).
  • Data sets can now be selected using wildcard chars * and ?, so one could for example specify C?[Life*] to get C1[Lifetime], C2[Lifelink], etc.

Actions

  • nastruct:
    • Add Zp calculation (3DNA style).
    • Better determination of base pairing; can now recognize non-WC base pairs.
    • Improved determination of base pair steps.
  • check: Add around <mask> functionality to check command to restrict part of the system checked.

Analysis

  • remlog: Ability to determine stats for different dimensions in remlog analysis.
  • kde: Fix to Kullback-Liebler divergence analysis in kde that occasionally resulted in 'nan' being written.
  • ired
    • Fixes for the relaxation calculation (integration of Cm(t) and calculation of Cj(t)).
    • Add full delta*S^2 matrix output option, ds2matrix <file>.
  • avg: oversets keyword; can now calculate average over multiple sets (as opposed to average of each individual set).
  • cluster: Fixes to dpeaks clustering. Add option to choose points manually, choosepoints manual via options distancecut <distcut> and densitycut <densitycut>. Probably more reliable than choosepoints auto at the moment.
  • calcstate: Assign states to frames based on data set criteria; resulting sets can be used in e.g. lifetime analysis.
  • multicurve: Non-linear curve fitting for multiple input data sets.
  • wavelet: Wavelet analysis on Cartesian coordinates.

As of May 1, 2015

  • Ability to perform math from command line, including limited ability to perform math on 1D data sets.
  • curvefit: Non-linear curve fitting.
  • cluster:
    • k-means clustering, [kmeans clusters <n> [randompoint [kseed <seed>]] [maxit <iterations>]
    • Can visualize pairwise distance matrix from cluster analysis in 2D (drawgraph) or 3D (drawgraph3d).
  • grid: Non-orthogonal grids; new keyword boxref). Usage: grid <filename> boxref <ref name/tag> <nx> <ny> <nz>