Preparing a molecular dynamics workflow once is manageable. Repeating it for dozens of starting conformations—or for several related proteins—can quickly become tedious. Each manual setup adds another opportunity to choose a different option, misplace an input, or lose track of which result belongs to which starting structure.
GROMACS Wizard’s batch workflow addresses this organizational problem: prepare a batch of related projects, then run minimization, equilibration, and simulation across the batch. The key is to decide what kind of batch you have before you start.
First, choose your batch type
One system, many conformations: Use this route when the molecular system is the same but you want to begin from different structures. You can select a set of conformations or a trajectory (a path). Each selected conformation—or each frame in the path—becomes the initial state for a separate subproject. This can be useful when comparing outcomes from different starting states or preparing inputs for workflows such as umbrella sampling.
If you already have a trajectory, open it in SAMSON or drag it into the application. To use only selected frames, inspect the trajectory and create conformations for the frames you want. Alternatively, create conformations from the full path and remove the ones you do not need.
Many different systems: Prepare each system separately first. Then place the resulting -prepare folders together in one batch folder. You can keep their existing names or rename them—for example, using PDB identifiers. Later, select From batch folder as the input. This approach is useful when you want to apply the same workflow settings to several prepared systems.
Make the box choice deliberately
For a batch of conformations of one system, the periodic-box setting affects both consistency and computational cost:
- Box lengths sets a box based on all conformations or the full path. It provides the same box size across the batch. Because the box must accommodate the conformations, a large or extended state can determine the dimensions for every subproject.
- Solute-box distance sets 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, potentially reducing computational time.
In practical terms: choose shared box lengths when having the same box size matters; choose a per-conformation distance when individual box sizes are acceptable and compact states may benefit from smaller boxes. After setting the box, use the slider in the Batch preparation area to check how it fits the different conformations.
Prepare once, then carry the batch through the workflow
For the conformations route, open the GROMACS Wizard’s Prepare tab, set the molecular system, enable Batch preparation, and select either the conformations or trajectory path. Set the force field and solvent, specify ions, choose the box approach, and prepare. Each numbered subfolder in the resulting batch project represents a separate project.
For subsequent steps—energy minimization, NVT equilibration, NPT equilibration, and production MD—use From batch folder as the input type. The auto-fill button can set the input based on the previous run.
You can launch the batch locally or in the cloud. A separate job is created for each subfolder. Local jobs can be monitored in the Local jobs window, where you can review status, change priority, stop or cancel jobs, import results, or open job folders. Cloud jobs can be monitored in the Cloud jobs window and can be stopped or canceled, downloaded, and imported.
A useful consistency check for mixed-system batches
When batching different systems, check that your molecular dynamics parameters do not rely on index groups or position restraints (POSRES records) that exist in only one system. Such system-specific settings may not be appropriate across the entire batch. This is particularly worth checking when using advanced options; the documentation notes these features are not often needed for simple protein systems.
A short pre-run checklist can prevent avoidable setup problems: confirm that every input belongs in the intended batch, decide whether your members are conformations or distinct prepared systems, choose a box strategy that fits your goal, and review any system-specific parameters before submitting jobs.
For the complete walkthrough, see the GROMACS Wizard batch computations tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.