A general-purpose script for common calculations with fDynamo

1. Clone the repository in your preferred location. Change directory to the new folder.
2. Compile DYNAMON with a Fortran compiler. Tested with gfortran.
3. For a better usability, source the file dynamon.rc in your .bashrc. The $DYNAMON variable will be set to the installation directory and the bin folder appended to your $PATH

git clone /~https://github.com/boneta/dynamon
cd dynamon
make -C src
source dynamon.rc

Only compiled once and configured at runtime on every execution!
For more information, see the documentation.

dynamon [.dynn] [[--option arg] ...]

Two non-exclusive ways of pass specific calculation options:

• With an input file (.dynn)
• Through command line arguments

For every system to work with a binary file (.bin) and a selection file (.dynn) with QM and NOFIX atoms are needed. Every calculation starts from a structure file (.crd).

Additionally, a PyMOL plug-in is available to helpful with the system setup.