smc-lammps documentation

smc-lammps is a python package that uses LAMMPS to perform coarse-grained Molecular Dynamics simulations of SMC complexes.

For information about installation and usage, view the README on github.

Workflow

The diagram below shows the basic program flow of smc-lammps.

■ smc-lammps    ■ LAMMPS

digraph workflow { bgcolor="transparent" rankdir=LR ranksep=0.8 nodesep=0.5 node [ shape=box, style="rounded,filled", fontname="Helvetica", fontsize=11, margin="0.2,0.1" ] edge [ fontname="Helvetica", fontsize=10 ] // Python (smc-lammps) nodes - blue parameters [label="User Input\n(parameters.py)", fillcolor="#e8f4f8", color="#5ba4b5"] vmd [label="Open in VMD", fillcolor="#e8f4f8", color="#5ba4b5"] analyze [label="Analyze SMC/DNA\npositions", fillcolor="#e8f4f8", color="#5ba4b5"] // LAMMPS nodes - orange inputs [label="LAMMPS Input Files\n(positions, coefficients,\nSMC states)", fillcolor="#fff3e0", color="#e67e22"] inputlmp [label="LAMMPS code\n(input.lmp)", fillcolor="#fff3e0", color="#e67e22"] outputs [label="Output Files\n(output.lammpstrj,\napo/atp/adp snapshots)", fillcolor="#fff3e0", color="#e67e22"] // Python edges - blue parameters -> inputs [label="--generate", color="#5ba4b5", fontcolor="#3d7a8a"] outputs -> vmd [label="--visualize", color="#5ba4b5", fontcolor="#3d7a8a"] outputs -> analyze [label="--post-process", color="#5ba4b5", fontcolor="#3d7a8a"] // LAMMPS edges - orange inputs -> outputs [label="--run", color="#e67e22", fontcolor="#c45a00"] inputlmp -> outputs [color="#e67e22"] }

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