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GROMACS Wizard - Periodic boundary conditions#

This page explains the box shapes available in GROMACS Wizard and the minimum-image rule you need to keep in mind when choosing box dimensions.

Use it together with Step 1: Prepare when you are deciding how to build the simulation box.

Before you start#

  • Read this page alongside Step 1: Prepare, because box-shape choices matter while you are setting up the system.
  • Focus first on two decisions: which unit-cell shape best fits your solute, and whether the box leaves enough distance to satisfy the minimum image convention.
  • If you are preparing a spherical solute in solvent, pay special attention to the rhombic dodecahedron and truncated octahedron examples below.

Unit cells#

"GROMACS uses periodic boundary conditions, combined with the minimum image convention: only one – the nearest – image of each particle is considered for short-range non-bonded interaction terms. For long-range electrostatic interactions, this is not always accurate enough, and GROMACS therefore also incorporates lattice sum methods such as Ewald Sum, PME and PPPM." (GROMACS Manual: Periodic boundary conditions)

GROMACS Wizard supports the following shapes for space-filling unit cells:

Unit cell shape Representation
Cubic Cubic
Orthorhombic Orthorhombic
Triclinic Triclinic
Rhombic dodecahedron Rhombic dodecahedron
Truncated octahedron Truncated octahedron

You choose the unit cell shape and its size when preparing a system:

Choose unit cell

The rhombic dodecahedron and the truncated octahedron are closer to being a sphere than a cube is, and are therefore better suited to the study of an approximately spherical macromolecule in solution since fewer solvent molecules are required to fill the box given a minimum distance between macromolecular images. The rhombic dodecahedron is the smallest and most regular space-filling unit cell. The volume is 71% of the volume of a cube having the same image distance. This saves about 29% of CPU time when simulating a spherical or flexible molecule in a solvent.

Two options for initial fitting of the box based on the system are available:

  • Box lengths – specify the box size. When fitted, it will fit tightly to your system – you will need to increase the size as needed to ensure the minimum image convention. This option also allows you to move the box to position the system in it. For the batch project, the initial box size is determined based on all the conformations or the whole path – choose this option if you want the box size to be the same for the whole batch.
  • Solute-box distance – specify the distance between the system (solute) and the box. At least 1 nm is recommended to ensure the minimum image convention. For the batch project, the box sizes will be different for each conformation or frame of the path.

Note

GROMACS always keeps the particles in a brick-shaped volume for efficiency. When loading GROMACS results, SAMSON will try to automatically detect the type of the unit cell of the system, but you can always modify it in the importer dialog that appears when loading GROMACS trajectories.

Please refer to GROMACS Manual: Periodic boundary conditions for more information on periodic boundary conditions and unit cell shapes.

Minimum image convention#

When periodic boundary conditions are used, it is crucial to satisfy the minimum image convention. In practice, your solute should never interact with its own periodic image; otherwise the forces may be wrong. A practical rule of thumb is to leave at least 1.0 nm between the solute and the box boundary, which creates at least 2.0 nm between periodic images of the solute.

Please refer to GROMACS Manual: Cut-off restrictions for more information.