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b35_N200_L500.data: Initial condition of the system that defines

  • Number of atoms, bonds, angles
  • Types of atoms, bonds, angles
  • 10 extra bond per atom tells the simulator to allocate extra memory for the reversible bonds that the sticker beads will form during the simulation
  • Dimension of cubic simulation box
  • Masses of the bead types
  • Coordinate of the atoms
  • Bonds (connectivity within chains)
  • Angles (between permanently bonded beads)

N200_Rg_L400.colvars: Colvars (collective variable) file that define the bead IDs (middle bead of each chain) to compute the radius of gyration of the system. fix colvars module uses this file to run metadynamics simulation.

b35_N200_L500.in: Input script for running Langevin Dynamics simulations using LAMMPS. Here we are modeling dynamic bond formation between two polymer types.

Simulation Overview

  • Temperature: 310 Kelvin
  • Duration: 100 million timesteps
  • Units: Real (energy in kcal/mol, distance in Angstroms, etc.)
  • Boundary Conditions: Periodic in all dimensions
  • Atom Style: Full (considering molecular bonds and angles)
  • fName is a string used to name output files

Simulation Steps

Initial condition: Read initial configurations (atom positions, bonds, angles) from b35_N200_L500.data

Force Fields and Interactions

  • Neighbor lists are constructed with a 1.9 distance bin
  • Angle force fields use a cosine functional form
  • Bonded interactions are defined using a hybrid style combining harmonic and harmonic/shift/cut
  • Lennard-Jones potential is used for non-bonding interactions with a cutoff of 25 Angstroms
  • bond/create/random and bond/break commands manage the dynamic creation and breaking of bonds within defined types and groups, based on distance criteria

Minimization and Equilibration

  • The system is minimized to converge forces to 1.0e-4 and energies to 1.0e-6
  • A Langevin thermostat is used for temperature control, incorporating stochastic dynamics with a damping parameter of 500
  • The system is evolved using the NVE ensemble
  • Perform the main simulation run for 100 million steps to observe clustering dynamics

Output and Data Handling

  • Generate detailed logs (${fName}.log) and system thermodynamics reports (Thermo_${fName}.dat)
  • Periodically dump coordinates (traj_${fName}.dump) for trajectory visualization
  • BondData_${fName}.dat tracks bond formations and breaks
  • Periodically dump restart files (${fName}_*.restart) to save system's configurations which can be used to analyze the cluster topology
  • Execute balance (comm_style tiled and fix balance) and communication management to optimize parallel computation load