/cpptraj

Biomolecular simulation trajectory/data analysis.
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README.md

CPPTRAJ

CPPTRAJ is a program designed to load and analyze molecular dynamics trajectories and relevant data sets derived from their analysis. It is a C++ rewrite of the PTRAJ trajectory analysis code from Amber.

Note that the GitHub version of CPPTRAJ should be considered BETA.
The official AmberTools release version of CPPTRAJ can be found at the Amber website.

For more information see the following publication:

Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem. Theory Comput., 2013, 9 (7), pp 3084-3095.

Build Status

Build Status Windows Build Status

PYTRAJ Compatibility Status

Pytraj GitHub CircleCI

Disclaimer and Copyright

CPPTRAJ is Copyright (c) 2010-2016 Daniel R. Roe. The terms for using, copying, modifying, and distributing CPPTRAJ are specified in the file LICENSE.

Installation & Testing

Run ./configure --help for a short list of configure options. ./configure --full-help will list all available configure options. By default, CPPTRAJ requires the following libraries:

  • NetCDF
  • BLAS
  • LAPACK
  • ARPACK
  • Bzip2
  • Gzip

For NetCDF trajectory output when processing trajectories in parallel, parallel NetCDF is also required (MPI build only).

./configure gnu should be adequate to set up compilation for most systems. For systems without BLAS/LAPACK/ARPACK and/or NETCDF libraries installed, the -amberlib flag can be specified to use the ones already compiled in an AmberTools installation ($AMBERHOME must be set), e.g. ./configure -amberlib gnu. For multicore systems, the -openmp flag can be specified to enable OpenMP parallelization, e.g. ./configure -openmp gnu. An MPI-parallelized version of CPPTRAJ can also be built using the -mpi flag. CPPTRAJ can be built with both MPI and OpenMP; when running this build users should take care to properly set OMP_NUM_THREADS if using more than 1 MPI thread per node.

The configure script by default sets everything up to link dynamically. The -static flag can be used to force static linking. If linking errors are encountered you may need to specify library locations using the --with-LIB= options. For example, to use NetCDF compiled in /opt/netcdf use the option --with-netcdf=/opt/netcdf. Alternatively, individual libraries can be disabled with the -no<LIB> options.

After configure has been successfully run, make install will compile and place the cpptraj binary in the bin/ subdirectory. It is highly recommended that make check be run as well to test the basic functionality of CPPTRAJ.

CPPTRAJ Authors

Lead Author: Daniel R. Roe (daniel.r.roe@gmail.com)
Department of Medicinal Chemistry
University of Utah, Salt Lake City, UT.

CPPTRAJ is based on PTRAJ by Thomas E. Cheatham, III (University of Utah, Salt Lake City, UT, USA) and many routines from PTRAJ have been adapted for use in CPPTRAJ, including code used in the following classes: Analysis_CrankShaft, Analysis_Statistics, Action_DNAionTracker, Action_RandomizeIons, Action_Principal, Action_Grid, GridAction, Action_Image, and ImageRoutines.

Contributors to CPPTRAJ

  • James Maier (Stony Brook University, Stony Brook, NY, USA)
    Code for calculating J-couplings (used in Action_Jcoupling).

  • Jason M. Swails (University of Florida, Gainesville, FL, USA)
    Action_LIE, Analysis_RunningAvg, Action_Volmap, Grid OpenDX output.

  • Jason M. Swails (University of Florida, Gainesville, FL, USA)
    Guanglei Cui (GlaxoSmithKline, Upper Providence, PA, USA)
    Action_SPAM.

  • Mark J. Williamson (Unilever Centre for Molecular Informatics, Department of Chemistry, Cambridge, UK)
    Action_GridFreeEnergy.

  • Hannes H. Loeffler (STFC Daresbury, Scientific Computing Department, Warrington, WA4 4AD, UK)
    Action_Density, Action_OrderParameter, Action_PairDist.

  • Crystal N. Nguyen (University of California, San Diego)
    Romelia F. Salomon (University of California, San Diego)
    Original Action_Gist.

  • Pawel Janowski (Rutgers University, NJ, USA)
    Normal mode wizard (nmwiz) output, original code for ADP calculation in Action_AtomicFluct.

  • Zahra Heidari (Faculty of Chemistry, K. N. Toosi University of Technology, Tehran, Iran)
    Original code for Analysis_Wavelet.

  • Chris Lee (University of California, San Diego) Support for processing force information in NetCDF trajectories.

  • Steven Ramsey (CUNY Lehman College, Bronx, NY) Enhancements to entropy calculation in original Action_Gist.

  • Amit Roy (University of Utah, UT) Code for the CUDA version of the 'closest' Action.

Various Contributions

  • David A. Case (Rutgers University, Piscataway, NJ, USA)
  • Hai Nguyen (Rutgers University, Piscataway, NJ, USA)
  • Robert T. McGibbon (Stanford University, Stanford, CA, USA)

Code in CPPTRAJ that originated in PTRAJ

  • Holger Gohlke (Heinrich-Heine-University, Düsseldorf, Germany)
    Alrun N. Koller (Heinrich-Heine-University, Düsseldorf, Germany) Original implementation of matrix/vector functionality in PTRAJ, including matrix diagonalization, IRED analysis, eigenmode analysis, and vector time correlations.

  • Holger Gohlke (Heinrich-Heine-University, Düsseldorf, Germany)
    Original code for DSSP (secstruct).

  • Michael Crowley (University of Southern California, Los Angeles, CA, USA)
    Original code for dealing with truncated octahedral unit cells.

  • Viktor Hornak (Merck, NJ, USA)
    Original code for mask expression parser.

  • John Mongan (UCSD, San Diego, CA, USA)
    Original implementation of the Amber NetCDF trajectory format.

  • Hannes H. Loeffler (STFC Daresbury, Scientific Computing Department, Warrington, WA4 4AD, UK)
    Diffusion calculation code adapted for use in Action_STFC_Diffusion.

External libraries bundled with CPPTRAJ

Documentation

The main documentation for CPPTRAJ usage is in the AmberTools user manual, available from the Amber website or from the AmberTools distribution in $AMBERHOME/doc. There is also limited help for commands in interactive mode via help [<command>]; help with no arguments lists all known commands.

Code documentation can be generated via Doxygen by typing make docs. This will install HTML and Latex documentation at doc/html/index.html and in the doc/latex respectively. A limited developers guide is available in Lyx/PDF formats in the doc/ subdirectory.