Example open source code for the single-molecule binding observables mentioned in 'Physical modelling of multivalent interactions in the nuclear pore complex': https://doi.org/10.1101/2020.10.01.322156

Ensure you have the LAMMPS 2016 (or above) version when running these simulations https://lammps.sandia.gov/.

Additionally, ensure that the morse pair potential is available through following the steps outlined in: https://lammps.sandia.gov/doc/pair_morse.html.

The code included in this repository is for an F6A chain (with six cohesive blocks, in the 4 amino acids per bead (4apb) coarse graining) and a patchy-particle (NTF2) with two cohesive binding sites.

This is a file containing the initial condition for the simulations.

(1) 30 particles belong to the F6A polymer. (2) 3 particles belong to the patchy particle. (3) They reside in a box (centered about the origin) with dimensions V = L^3 = 25^3.

This performs an initial simulation to check the initial conditions. It outputs a restart file to be used for the production simulation.

If you have a LAMMPS executable called lmp_serial then run this simulation on the command line as:

lmp_serial -in in.start_up_4apb

This performs a much longer production simulation where the 'xyz' file contains the time trajectory of the all the bead coordinates. Note: you must have successfully run in.start_up_4apb first.

lmp_serial -in in.resume_4apb

This calculates the single-molecule kD.

What you should run on the command line:

perl do_kD.pl simulation_trajectory.xyz 2 5 1.4 25 4 2

The arguments are (1) xyz file name (2) particle type for the polymer cohesive block (3) particle type for the particle cohesive patch (4) cutoff (r_0) between a particle patch of diameter 0.38 nm and a polymer bead of diameter 1.02 (5) The box length L = 25 nm (6) the coarse graining of the polymer (4 = 4apb) (7) the number of patches on the patchy-particle = 2 in this case.

This calculates the single-molecule koff.

What you should run on the command line:

perl do_koff.pl simulation_trajectory.xyz 2 5 1.4 25 4 2

with the same parameters as for do_kD.pl.