What does this code do
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The code simulates coarse-grained ligand-receptor binding of ligand-decorated virus particles interacting with a cell wall
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Users can input control parameters such as ligand-receptor binging affinity (E: 1 - 10 KbT), number of ligand-decorated virus particles (S: 1 - 1000), concentration of ligand-decorated virus particles (C: 0.3 - 9 nM), receptor-receptor spacing (W: 10 - 200 nm) and simulation run time (T: 100 - 5000 milliseconds).
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Outputs are the number of bound receptor at equilibrium and simulation snapshots (in lammps movie format). The viruses are modeled after P22 virus-like particles (VLPs) of diameter 60 nanometers, and ligands represent smaller nanoparticles of 6 nanometer diameter. Each virus is fully decorated with 60 ligands.
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Simulations are performed using LAMMPS; pre- and postprocessing are done using C++ codes.
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At the end of simulation run, which will take close to 60 minutes, the number of bound receptors will be printed in bin/outfiles.
For further details please refer to the documentation
- First, git clone the project:
https://github.com/softmaterialslab/nanobind.git - Go to the root director:
cd /nanobind - Install the project:
make cluster-install - Submit a job:
make cluster-submit - To change the default parameters of E (ligand-receptor binding strength, KbT), S (number of virus-ligand complexes), T (simulation runtime, milliseconds) or C (concentration of virus-ligand, nanomolar);
make cluster-submit E=5 S=125 T=100 C=0.3 - All outputs from the simulation will be stored in the bin folder when the simulation is completed.
- If you want to clean everything and create a new build, use:
make clean
- First, git clone the project:
https://github.com/softmaterialslab/nanobind.git - Load necessary modules:
module load gsl && module load mpi/openmpi-x86_64 && module load boost/1_67_0 - Also make sure to export OMP_NUM_THREADS environment variable with maximum threads available in your CPU:
export OMP_NUM_THREADS=16 - Install the project:
make local-install - Run the simulation:
make local-run-parallel LAMMPS_EXE=lmp_g++ - Run the simulation in parellel mode:
make local-run-parallel LAMMPS_EXE=lmp_g++ MPI_EXE=mpirun NODESIZE=4 - To change the default parameters of E (ligand-receptor binding strength, KbT), S (number of virus-ligand complexes), T (simulation runtime, milliseconds) or C (concentration of virus-ligand, nanomolar);
make local-run-parallel E=5 S=125 T=100 C=0.3 - All outputs from the simulation will be stored in the bin folder when the simulation is completed.
- If you want to clean everything and create a new build, use:
make clean - If you want to clean data, use:
make dataclean