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Directory description

This example can be found in the directory examples/lysozymes/128_ph6/. The full list of directories in examples/lysozymes includes:

prepare_grids_and_ecm/ Directory to generate the data files (pdbs, grids and effective charges) into the data_grid/ directory
data_grid/ Data files (pdb and input files) needed for running the examples
128_ph6/ Results of a SDAMM run where all lysozymes are at a constant protonation state (ph6)
128_flex/ Results of a SDAMM run where lysozymes can change protonation states (ph3, ph6 or ph9)
doc/ This documentation
unit-test/ For developers, regression tests for different combinations of interactions. The grids need be generated first
Details of the input

This example is a SDAMM-type simulation with 128 lysozyme molecules. Lysozymes are in a simulation box of 460 Å^3 at a concentration of 15 g/L.
All solutes are in a protonation state corresponding to pH 6.

The simulation uses Periodic Boundary Conditions (PBC) in all three directions. The solutes are interacting through the following terms:
Running the examples

Assure you have compiled all the executables and tools in sda_flex/bin/ first (refer to the compilation section).

Then go to the examples/lysozymes/128_ph6 directory and execute the run sda_flex:

cd 128_ph6/
../../../bin/sda_flex lys_128_ph6.in > my_out_128_ph6

You might want to check the README files for an exemplary analysis of the trajectory.

We advise to perform calculations in a separate directory, so that the original output files will not be overwritten.

This folder contains also examples of usage of tools:

Output and results

This simulation is described in detail in: Mereghetti, P., Gabdoulline, R. R., and Wade, R. C. (2010). Brownian dynamics simulation of protein solutions: structural and dynamical properties. Biophysical journal, 99(11), 3782–91. doi:10.1016/j.bpj.2010.10.035. Please note that these simulations were run with different parameters from those used in the example. The example is a smaller system (128 proteins instead of 512 proteins) and different parameters are used for computing the interactions between proteins.

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