What does this code do
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The code simulates the assembly of two types of charged nanoparticles (NPs) into aggregates mediated by smaller, oppositely-charged linkers under different ionic physiological conditions.
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The NPs are modeled after P22 virus-like particles (VLPs) of diameter 56 nanometers, and linkers represent smaller nanoparticles (dendrimers) of 6 nanometer diameter.
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Simulations are performed using LAMMPS; pre- and postprocessing are done using C++ codes.
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Simulation results are tested and validated using SAXS and dynamic light scattering measurements of the VLP aggregates; experiments also guide the model design.
Local install and testing (after loading the needed modules):
- module load gsl && module load openmpi/3.0.1 && module load boost/1_67_0
- from root (bnsl) directory: make local-install
- cd bin/
- to test 1:1 systems: make run-preprocessor r=1
- to test 1:4 systems: make run-preprocessor r=4