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README
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_______________________________________________________________________
CPPTRAJ: 2014 - README FILE
_______________________________________________________________________
About CPPTRAJ
---------------------------------------
CPPTRAJ is code intended to be a complement and perhaps eventually a
replacement for PTRAJ, the MD trajectory analysis software that comes
packaged with AmberTools.
CPPTRAJ is a complete rewrite of the PTRAJ code in C++, the intent being
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.
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 (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 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 $AMBERHOME/doc. There is also
limited help for commands in interactive mode:
help [<command>]
'help' with no arguments lists all known commands.
Code documentation can be generated via Doxygen by typing 'make docs'. This
will install HTML and Latex documentation at doc/html/index.html and in
the doc/latex respectively. A limited developers guide is available in
Lyx format in doc/CpptrajDevlopmentGuide.lyx.
Installation & Testing
----------------------------------------
CPPTRAJ by default will be installed as part of AmberTools. CPPTRAJ can also
be installed as a stand-alone program. The configure script in this directory
is for stand-alone compilation only. Run './configure --help' for the complete
list of configure options.
'./configure gnu' should be adequate to set up compilation for most systems.
For systems without BLAS/LAPACK/ARPACK and/or NETCDF libraries installed,
the '-amberlib' flag can be specified to use the ones already compiled in
an AmberTools installation ($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_local' will
compile and place the cpptraj binary in the bin/ subdirectory.
To test the binary in the bin/ directory either run 'make check_local' or
change to the 'AmberTools/test' directory and run 'make test.standalone'.