Ignoring periodic boundary conditions

gorder fully supports the handling of orthogonal (i.e., rectangular cuboid) periodic boundary conditions (PBC) applied in all three dimensions. If your simulation box is orthogonal and PBC are applied in all three dimensions, you can use a raw trajectory generated by Gromacs directly, without worrying about making molecules whole in the simulation box or dealing with other PBC-related issues. gorder will handle everything automatically.

However, if your simulation box is not orthogonal, gorder cannot properly treat the system and you will get an error. In such cases, you must instruct gorder to ignore periodic boundary conditions by adding the following line to your input YAML file:

handle_pbc: false

When this option is set to false, gorder will disregard periodic boundary conditions and the presence of any simulation box. Effectively, it will treat the atoms in your system as if they exist in an infinite, unbound environment. When ignoring PBC, it is crucial to ensure that all lipid molecules in your system are whole in every frame of the input trajectory. If your molecules are "broken" at the box boundaries, you may silently get completely incorrect results! When ignoring PBC, you will always get a warning reminding you to make molecules whole:

[W] Periodic boundary conditions ignored. Lipid molecules must be made whole!

With Gromacs, you can make molecules whole using the following command:

gmx trjconv -s TPR_FILE -f XTC_FILE -pbc mol -o OUTPUT_XTC_FILE

The resulting OUTPUT_XTC_FILE should then be used as the trajectory input for gorder.

You can of course choose to ignore PBC for any system, even if it has an orthogonal box.

Note: You do not necessarily have to set handle_pbc to false when working with an orthogonal box with PBC applied in fewer than three dimensions. However, such systems are untested, so proceed with caution. In case you are not sure the analysis is correct, try using a trajectory with whole molecules, set handle_pbc to false, and check whether the results change.

Limitations when ignoring PBC

Be aware of the following limitations when PBC are ignored:

  1. Order parameters for individual leaflets
    Ensure that your membrane is fully within the simulation box. For example, if your membrane lies in the xy-plane, ensure it does not extend beyond the limits of the simulation box in the z-dimension or appear fragmented across the periodic boundary. Failing to meet this requirement may result in entirely incorrect lipid leaflet assignments. To avoid issues, you may want to center the membrane in the simulation box before running the analysis.

  2. Ordermap dimensions
    When constructing ordermaps, you cannot automatically derive their dimensions from the simulation box because it is ignored. You must specify the dimensions manually. Forgetting to do this will result in an error. See this section of the manual for instructions on setting dimensions.

  3. Reference points for geometry selections
    When calculating order parameters for a specific region, you cannot use the dynamic center of the simulation box as the reference point because gorder ignores box information. If this constraint is violated, you will get an error. However, you can still use static coordinates or the dynamic center of geometry as the reference point. If using the dynamic center of geometry, ensure that your selected atoms for center calculation are made whole, i.e., are not broken at the simulation box boundary.

  4. Using structures and trajectories not generated by Gromacs
    While gorder (and Gromacs) interpret [0, 0, 0] as the origin of the simulation box (i.e., one of its corners), some other software treats [0, 0, 0] as the center of the simulation box. This difference can cause issues when ignoring periodic boundary conditions, as particles may not be correctly wrapped into the box as gorder expects. In such cases, you must translate the system by half of box size in each dimension so that [0, 0, 0] aligns with the origin of the simulation box (rather than its center) before running the analysis.