Preparing a molecular dynamics workflow repeatedly can be tedious—and it is easy to introduce small inconsistencies when each project is configured by hand. GROMACS Wizard batch computations address this problem by letting you apply the same workflow to many starting conformations of one system, or to several separately prepared systems. The key is to choose the right batch structure and make a few decisions about inputs and box settings before launching jobs.
First decide what belongs in the batch
There are two useful cases:
- One system, many conformations: Each conformation—or each frame in a selected trajectory—becomes the initial state for a separate subproject. This can be useful when comparing starting poses or preparing multiple states for a workflow such as umbrella sampling.
- Several different systems: Prepare each system individually, then place the resulting
-preparefolders together in a batch folder. The later steps can use that folder as their input.
These approaches solve different organization problems. A trajectory is a natural input when the molecular system stays the same and the coordinates vary. Separate prepared folders are the appropriate route when the systems themselves differ.
For conformations: choose the states deliberately
For a trajectory-based batch, load the trajectory into SAMSON, or create conformations using the available tools and extensions. You do not have to use every trajectory frame: you can inspect frames and create conformations for selected ones. Alternatively, create conformations from the entire path and delete the states you do not want to include.
In GROMACS Wizard, open the Prepare tab, set the structural model as the molecular system, and enable Batch preparation. Select either a set of conformations or a path, then click Set conformations or a path. The displayed count and slider help you confirm what will be included before preparation.
Next, configure the force field, solvent, ions, and any custom index groups as you would for a single project. Think of this as setting up a consistent recipe: the batch applies the workflow across its starting states, so make sure the selected inputs and settings match the question you want to investigate.
The box-setting choice affects the whole batch
For conformations, the periodic box can be configured in two ways:
- Box lengths: Set a common box based on all the conformations or the full path. This keeps the box size the same throughout the batch. Because the fitted box may be tight, increase its size as needed to satisfy the minimum image convention.
- Solute-box distance: Set the distance between the solute and the box separately for each conformation. The documentation recommends at least 1 nm to help ensure the minimum image convention. More compact conformations can then use smaller boxes, which can reduce computational time.
In practice, the decision is about consistency versus per-state sizing: choose common box lengths when having the same box across the batch matters; choose a solute-box distance when different box sizes are acceptable. Use the slider in the Batch preparation section to check how the box fits the conformations before clicking Prepare.
For different systems: keep shared settings truly shared
Prepare each system separately, put the resulting prepared folders into one batch folder, and optionally rename the subfolders—for example, with PDB identifiers. Those names are preserved in later steps. When running minimization or subsequent stages, select From batch folder and choose this folder.
One important safeguard: avoid MD parameters that refer to index groups or position-restraint records present in only some batch members. Such system-specific settings may not apply to every project in the batch.
Run and monitor the batch
After preparation, the batch contains numbered subfolders for conformations, or the prepared subfolders for different systems. Continue through energy minimization, NVT equilibration, NPT equilibration, and production molecular dynamics using From batch folder as the input. The auto-fill button can select the previous step’s output automatically.
Jobs can run locally or in the Cloud. A separate job is created for each subfolder. Local jobs can be monitored and managed in the Local jobs window; Cloud jobs can be monitored and managed in the Cloud jobs window. This per-subproject structure makes it easier to see which members are progressing and to work with individual results.
Batching is most useful when the workflow should be consistent, but it does not remove the need to check that each starting state and shared setting is appropriate. A quick review of the selected conformations, box fit, and any system-specific parameters can prevent avoidable setup problems before the full batch runs.
Learn more in the GROMACS Wizard batch computations tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.