Constructing Disordered Systems for Coarse-Grained Modeling

Disordered molecular systems can be assembled for coarse-grained modeling in the Disordered System Builder Panel from a set of source all-atom molecules or a set of source molecules constructed from coarse-grained particles.

  • If you want to build the system from all-atom molecules, you can use the Maestro tools to build general types of source molecules, or use other tools that are designed for building specific types of molecules. For example, you can build polymers with the Polymer Builder Panel.
  • If you want to build the system from coarse-grained molecules, you can use the same tools to build the all-atom molecules, then convert them into particles in the Map Atoms to Particles Panel, and use the output from this panel as input to the Disordered System Builder panel. You can also import coarse-grained molecules for use with the Martini force field in the Import Martini Coarse-Grained Structures Panel, and use the entries for these molecules for building the system.

As the system you build is intended for coarse-grained modeling, the settings required may be different from those for all-atom modeling. The information given below outlines choices that should be made in the Disordered System Builder Panel.

If you built the system with coarse-grained molecules, or you built it with all-atom molecules and plan to convert it without doing any all-atom simulations, you should turn off the force field settings. Specifically, the following options should be turned off:

  • Prepare Desmond systems
  • Minimization
  • Monte Carlo simulated annealing

It is usually best to select cubic boundary conditions, unless the specific cell shape is advantageous for the study at hand.

The Disordered System Builder Panel launches a job that can take from a few minutes to many hours to complete. Selecting appropriate options involves a trade-off between the compactness of the resulting system and processing time. In practice, the resulting systems usually have low densities with significant amounts of unoccupied volume, due the challenge of packing molecules together in a limited amount of time.

The choice of nonbonded potentials (LJC or RH) strongly affects the options that produce good results. Clashes can be a major problem for LJC models, while they are much less so for RH models. Conversely, LJC systems can be constructed with excess volume and then compressed during a simulation, while RH models are best simulated starting from the correct volume. As a result, the strategies for reducing the volume are different for each model, and are reflected in the choice of options.

For LJC systems, a pragmatic approach is to accept excess volume in the Disordered System Builder stage to reduce processing time in the panel, and then compress out some of the excess volume during an equilibration portion of the Multistage Simulation Workflow (discussed in Setting Up the Coarse-Grained Simulation). The following settings in the Disordered System Builder have proven useful in some cases for LJC systems:

  • Initial state : Snapped to grid
  • Steric pack : off
  • Disorder options (click Disorder Options
    • Initial VdW scale factor : 0.7
    • Initial density : 0.5
    • Keep constant : VdW Scale factor
    • Placement attempts per molecule : 200.

The volume of the system is adjusted later in the actual simulation.

For RH systems, the lack of a truly excluded volume means that molecules can be packed together with significant overlap. For the simulations, the correct volume must be set, which affects the strategy used to build the system. Recommended settings in the Disordered System Builder for RH systems include:

  • Initial state : Amorphous
  • Steric pack : on
  • Disorder options (click Disorder Options
    • Initial VdW scale factor : 0.3
    • Initial density : 1.0
    • Keep constant : Density
    • Placement attempts per molecule : 200.

After the coarse-grained system has been set up, the volume of the system is adjusted to the appropriate value using the scale_simulation_box.py script, as described in Adjusting the Volume for a Repulsive Harmonic System.