This example can be found in the directory examples/lysozyme_mica.It demonstrates the adsorption process of HEWL to a mica-like surface as simulated with SDA. The setup of the simulations and the functionalities with respect to electrostatic and hydrodynamic interactions are described in Reinhardt M, Bruce NJ, Kokh D, Wade RC. Brownian Dynamics Simulations of Proteins in the Presence of Surfaces: Long-range Electrostatics and Mean-Field Hydrodynamics.
The following table gives information about the different subfolders in the example directory :
|prepare_grids_and_ecm/||Directory to generate the data files (pdbs, grids and effective charges) into the data_grid/ directory. There are two subfolders hewl and surface. Please run the prepare_surface_grids.sh in both directories. Make sure to set the correct path to the SDA installation.|
|data_grid/||Data files (pdb and input files) needed for running the example./td>|
|lys_20gL_completed/||Results of the example as it was run at HITS. Due to the large size of the trajectories and some grid files they are excluded from the software download. You can obtain theses result files of the example by running the get_Lysozyme_mica-data.sh script in the root directory of the example (this downloads a zip file from the URL: https://projects.h-its.org/sda/example/Lysozyme_mica/Lysozyme_mica-data.zip and unpacks it).|
|lys_20gL/||Directory to run the Lysozyme_mica example. It uses the run.sh command. Make sure you have set the correct path for the SDA installation.|
|doc/||Documentation of the Lysozyme mica example. The respective PDF is included in the distribution.|
Assure you have compiled all the executables and tools in sda_flex/bin/ first or refer to the compilation section.
Run first the script prepare_grids_and_ecm in the lys_20gL/hewl and lys_20gL/surface directory to generate the grids necessary to run this example. The grids will be copied to the data_grid directory.
Then go in the lys_20gL directory and run sda by executing the script run.sh.
You can check if the output files are similar to the ones generated at HITS: lys_20gL_completed/. Please note, that the run included from HITS was run with a higher timemax value (250000 vs 100000) and therefore is more detailed. Also, due to size contraints the trajectories andi large grid files are excluded from the software package. They can be downloaded as described above.
Note : you may need to adapt the shell scripts to your environment (location of APBS for instance)