Modeling tools for simulations of oligomers consisting of very-coarse-grained representations of Alpha-B Crystallin.
The program requires the Boost library, specifically the program options module.
Building and installation is done with CMake.
To configure, build and install in installdir, run
CXX=clang++ cmake -S . -B build -DCMAKE_INSTALL_PREFIX=[installdir] -DBUILD_TESTING=OFF
cmake --build build
cmake --install build
Example input files for running simulations can be found in scripts/examples/.
To see all configuration options, run
blobCrystallinOligomer -h
To run a simulation, enter
blobCrystallinOligomer -i [configuration file] > [log file]
Tcl scripts for VMD are available in scripts/vmd for viewing configurations.
To watch a simulation live, run
vmd -e [scripts dir path]/pipe.tcl -args [vmd scripts directory] [output filebase]
To watch a simulation that has finished, start VMD and run
set libdir [vmd scripts directory]
set filebase [output filebase
source [vmd scripts directory]/view_coors.tcl