openTRJ is an ensemble of programs to compute a few properties from MD simulation trajectories written in .dcd or .xtc format. It was created to treat systems undergoing self-aggregations, such as micelles, inverted micelles, aggregates of proteins. The compilation with no parameters create three programs:
- trjVoronoi which computes the Voronoi volumes using voro++
- trjProp which computes radius of gyration and aggregation properties
- trjSaxs which computes the Saxs or Sans profiles of the system
All programs require a .pdb file containing the coordinates of the whole system, including waters and ions if needed. trjVoronoi uses voro++ by Chris H. Rycroft to compute properties of molecular systems in solution from molecular dynamics trajectories obtained with GROMACS and NAMD.
This project was created to compute the self aggregation properties of large systems.
openTRJ uses standard cmake (version > 3.0) scripts to generate Makefiles. This means that a typical installation will consist in creating a build directory and running within
that directory a command such as 'cmake ..' followed by
make
make install
The code needs that the fftw3 libraries be installed on the system. If openMPI and opneMP are available the code is compiled for parallel runs.
openTRJ uses several features available with the C++11 standard, thus it will not compile with GNU g++ compilers earlier than 5.4. It has been successfully compiled on Centos, Debian and Mac OS X systems supporting those versions of the C++ compilers.
M. Marchi, A first principle particle mesh method for solution SAXS of large bio-molecular systems, J. Chem. Phys. 145, 045101 (2016).
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