Running molecular dynamics on several starting conformations can mean repeating the same setup steps again and again. That takes time—and makes it easier to miss a setting or handle one project differently from the others. Batch preparation in SAMSON’s GROMACS Wizard helps address this by creating a separate subproject for each starting state while letting you apply a shared workflow.
This is useful when you want to compare how one molecular system behaves from different conformations, such as selected frames from a trajectory. It also supports a different use case: processing several separately prepared systems with the same simulation settings. Choosing the right route at the outset keeps the batch organized and helps avoid assumptions that do not apply to every member.
First, decide what your batch represents
For one system with many conformations, start with a structural model and a set of conformations or a trajectory path. In the GROMACS Wizard’s Prepare tab, set the molecular system, enable Batch preparation, and select the conformations or path. Each selected conformation—or each frame in the path—becomes the initial state for a subproject.
If you only want certain trajectory frames, you do not have to use every frame. You can navigate to chosen frames in the Inspector and create conformations through Edit > Conformation. Alternatively, create conformations from the path in the Document view, then remove the ones you do not need. This gives you control over which starting states enter the batch.
Make an intentional box choice
One decision can affect every member of a conformation batch: how the periodic box is defined. Choose Box lengths when you want a common box size based on all the conformations or the whole path. The box can be fitted to the system, but a tightly fitted box may need to be increased to respect the minimum image convention. This option also lets you reposition the box around the system.
Choose Solute-box distance when you want the box size to be determined separately for each conformation. The documentation recommends a distance of at least 1 nm. This can give compact conformations smaller boxes, potentially reducing computational time, but the resulting box sizes will differ across the batch. Use the preparation slider to inspect how the box fits the conformations before proceeding.
When the batch contains different systems
For a collection of different proteins or other systems, prepare each system separately first. Then put the resulting -prepare folders together inside one batch folder. You can keep their existing names or rename them—for example, using PDB identifiers—and those names are preserved in later steps.
There is an important compatibility check here: avoid MD parameters that refer to index groups or position restraint (POSRES) records present in only some batch members. A setting that works for one system may not be valid for another. Shared parameters should be appropriate for every system in the folder.
Continue the workflow without reopening every project
After preparation, the batch project contains numbered subfolders, each representing a separate project. Run minimization, NVT equilibration, NPT equilibration, and production molecular dynamics using From batch folder as the input. The auto-fill button can set the input path based on the previous run.
Jobs can be launched locally or in the Cloud. A separate job is created for each subfolder. Local jobs can be monitored in the Local jobs window; Cloud jobs can be followed in the Cloud jobs window. This keeps the workflow organized while preserving each member as its own project.
A quick pre-run check: confirm whether you are batching conformations or different systems, inspect your box choice, and verify that shared parameters make sense for every subproject. For the complete workflow and interface details, see the GROMACS Wizard batch computations tutorial.
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