Preparing and running molecular dynamics simulations one project at a time can become repetitive when you have many starting conformations—or several related systems to process with the same settings. It is also easy to lose track of which input belongs to which run. GROMACS Wizard’s batch workflow helps organize these cases as a collection of separate subprojects, so you can prepare them together and launch later stages across the batch.
The first useful decision is what you are batching: one molecular system with many starting states, or multiple prepared systems. The distinction affects how you prepare the inputs and, especially, how you choose the periodic box.
One system, many starting conformations
This approach is useful when you want to apply the same workflow to several conformations of the same molecular system. The starting states can come from a trajectory or from individual conformations in SAMSON. To load an existing trajectory, use Home > File > Open or drag it into SAMSON.
If you only want selected trajectory frames, you do not have to use every frame. You can move through the trajectory with the Inspector and create conformations for chosen frames using Edit > Conformation. Alternatively, create conformations from the whole path using Path > Create conformations from path in the Document view, then remove the ones you do not need.
In the GROMACS Wizard’s Prepare tab, set the structural model as the molecular system and enable [Optional] Batch preparation. Select either a set of conformations or a trajectory path, then click Set conformations or a path. With a set of conformations, each conformation becomes the initial state of a subproject; with a path, each frame becomes an initial state. The displayed count and slider let you check the selected starting states before proceeding.
Continue with the usual preparation choices: force field and solvent, any needed custom index groups, and ions. Then decide how the periodic box should be defined. This choice is a practical trade-off:
- Box lengths: the box is based on all conformations or the whole path, so its size is the same throughout the batch. This is useful when consistent box dimensions matter. Because the box is fitted to the system, check that it is large enough for the minimum image convention.
- Solute-box distance: the box is sized separately for each conformation or frame. The documentation recommends at least 1 nm between solute and box to help ensure the minimum image convention. More compact conformations can use smaller boxes, which can reduce computational time.
Use the batch-preparation slider to inspect how the chosen box fits the different conformations. This is a simple check before committing to preparation, particularly if the starting states vary in shape or extent.
Several different systems
For multiple systems, prepare each one separately first. Put the resulting folders (with the -prepare suffix) into a shared batch folder. You can rename the subfolders, for example with PDB identifiers; their names are preserved in later steps. When you run minimization or another subsequent stage, choose From batch folder and select that folder.
One important compatibility check: avoid MD parameters that refer to index groups or position restraints specific to only one system in the batch. A setting that works for one member may not be present in the others. For a batch of different systems, use shared settings that are valid across the whole set.
Run the next stages together
After preparation, the workflow follows the familiar sequence: energy minimization, NVT equilibration, NPT equilibration, and production molecular dynamics. Set the input type to From batch folder; the auto-fill button can populate the input path from the previous run.
Batch execution still creates separate jobs for the subprojects. For local runs, each subfolder becomes a local job that you can monitor, reprioritize, cancel or stop, import, or open from the Local jobs window. Cloud runs likewise create a separate Cloud job per subfolder, with options to monitor, stop or cancel, download, and import the jobs.
Choose “From batch folder” to use the prepared batch as input for a workflow step.
A useful pre-run checklist: confirm that the selected conformations or systems are the intended inputs; choose a box strategy that fits your batch; check that settings are appropriate for every member; and verify that subsequent steps point to the batch folder. These checks help keep a multi-project workflow organized without changing the underlying steps of a single-project simulation.
For the full workflow and interface details, see the GROMACS Wizard batch computations tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.