CPPTRAJ

CPPTRAJ is a program designed to load and analyze molecular dynamics trajectories and relevant data sets derived from their analysis.

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.

About CPPTRAJ

CPPTRAJ is a rewrite of the PTRAJ trajectory analysis code in C++ that is part of AmberTools. The intent is to make the code more readable, leak-free, and thread-safe. The biggest functional change from PTRAJ is the ability to load and process trajectories with different topology files in the same run.

Build Status

Disclaimer and Copyright

CPPTRAJ is Copyright (c) 2010-2014 Daniel R. Roe. The terms for using, copying, modifying, and distributing CPPTRAJ are specified in the file LICENSE.

Contributors to CPPTRAJ

Lead Author: Daniel R. Roe ([email protected]) 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 by CPPTRAJ, including (but not limited to) code used in the following classes:

• Analysis_CrankShaft
• Analysis_Statistics
• Action_DNAionTracker
• Action_RandomizeIons
• Action_Principal
• Action_Grid
• Grid
• Action_Image
• ImageRoutines

Contributors

• 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). Action_Gist

The following people wrote code in PTRAJ which was eventually adapted for use in CPPTRAJ:

• 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.

Documentation

The main documentation for CPPTRAJ usage is in the AmberTools user manual, available with any AmberTools distribution in $AMBERHOME/doc. There is also limited help for commands in interactive mode:

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 format in doc/CpptrajDevlopmentGuide.lyx.

Installation & Testing

Run ./configure --help for the complete list of configure options.

./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.

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 '-noLIB' options.

After config.h has been successfully generated, make install will compile and place the cpptraj binary in the bin/ subdirectory.