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HFBI graphite interactions

This example can be found in directory examples/HFBI-graphite.
You need to run at least one time the script in prepare_grids_and_ecm/ to generate the grids and effective charges needed by the input files.

Directory description

data_grid/ Data files (pdb and input files) needed for running the examples
prepare_grids_and_ecm/ Directory to prepare grids and effective charges
run/ Directory to run the simulation
run/sdamm_out_hits Subdirectory containing the ouput files generated at HITS.
doc/ This documentation

Details of the input

This input will run a sdamm simulation of 100 hydrophobin molecules with a graphite surface.
Graphite is a neutral surface, therefore the interactions between hydrophobins and graphite include only soft-core repulsion, electrostatic desolvation and non-polar desolvation. However, the interactions among hydrophobins are represented fully, i.e., include the electrostatic term, soft-core repulsion, electrostatic desolvation and non-polar desolvation.
To represent these asymmetric interactions correctly in SDA, one can omit the electrostatic grid and the effective charges for the graphite surface.

Running the example

cd run/
./run_sdamm.sh

The script will run the simulation and generate a dcd format of the trajectory

Results of the simulation

You can compare the results with the output files in the subfolder: sdamm_out_hits/

A snapshot generated after the 25 ns of the multiple proteins run. It shows few interaction between the hydrophobins and the surface.
The simulation should be run more than 100 ns to see spefic interactions.

The results of similar simulations (run with some different parameter settings) are described in : Mereghetti and Wade, R. C. (2011). Diffusion of hydrophobin proteins in solution and interactions with a graphite surface. BMC Biophysics 2011, 4:9 doi:10.1186/2046-1682-4-9

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