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 |
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.
- Electrostatic
- Electrostatic desolvation
- Non-polar desolvation
- Soft-core (LJ) repulsion
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:
- generate_init_pos: generation of the initial configuration of the solutes inside a box
- analysis: computation of the diffusion coefficients from an SDAMM trajectory (see the script
analysis/analysis.sh)
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.