A simulation box can look like a simple setup choice, but getting it wrong can affect the physical meaning of a molecular dynamics run. If the box is too small, a molecule may interact with its own periodic image. If you are preparing several conformations, a box that fits one structure may not fit the rest. These are easy issues to overlook when the structure itself looks ready to simulate.
In GROMACS Wizard, box setup is part of preparing the system. The aim is to choose a unit cell and dimensions that include the selected structure while leaving enough space between the solute and the box boundaries. Here is a practical way to think through those choices before running preparation.
First, decide what must fit
Select the molecular system you intend to prepare, then define a box that includes every structure in that selection. This matters especially when a document contains multiple structural models. For a batch project based on conformations or a trajectory, consider the full set of structures—not just the one currently visible or selected in a viewer.
GROMACS Wizard supports cubic, orthorhombic, triclinic, rhombic dodecahedron, and truncated octahedron unit cells. The best choice depends on your system and workflow; the tutorial uses an orthorhombic cell as an example.
Choose how the box is fitted
There are two fitting approaches, and they answer slightly different needs:
- Solute-box distance: Specify the distance between the system and the box. The documentation recommends at least 1 nm to help satisfy the minimum image convention. For a batch, each conformation or trajectory frame can have a different box size.
- Box lengths: Specify the box dimensions. The fitted box initially follows the system closely, so you must increase its size to add the necessary space. For a batch, the initial dimensions are based on all conformations or the whole trajectory path, which is useful when you need the same box size throughout.
A helpful rule of thumb: choose Solute-box distance when a consistent buffer around each structure is your priority; choose Box lengths when keeping a common box size across a batch is important. Either way, check that the box includes all selected structures.
Why the extra distance matters
Periodic boundary conditions make the simulation behave as though copies of the box repeat in space. The minimum image convention is intended to prevent a solute from interacting with its own periodic image in a way that would make the calculated forces inappropriate. The tutorial recommends adding at least 1.0 nm between the solute and the box edge. In practical terms, that corresponds to at least 2.0 nm between periodic images of the solute.
This is a recommendation, not a universal guarantee for every system or force field. Molecules can change conformation, and a custom force field may call for checking its published guidance. Use the distance as a starting point, then make sure the box remains suitable for the system and the simulation settings you plan to use.
Before clicking Prepare
- Confirm that the selection contains the structures you mean to simulate.
- For batches, decide whether you prefer the same box dimensions or a separately fitted box for each conformation or frame.
- Check that there is adequate space between the solute and the box boundaries.
- If you plan to add ions, remember that solvent must also be added: ions replace water molecules during preparation.
Once the box and other preparation options are set, run preparation and review the output for warnings. The prepared system can then be imported into SAMSON for inspection before continuing to energy minimization.
For the full preparation workflow and details on force fields, solvent, and ions, learn more in the GROMACS Wizard preparation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.