Preparing a molecular-dynamics run is already a sequence of decisions. Repeating those decisions by hand for dozens of starting conformations—or for several related systems—adds effort and makes it easier to apply settings inconsistently. Batch preparation in SAMSON’s GROMACS Wizard helps organize that work: prepare a collection of starting states or prepared systems, then run the later stages across the batch.
The key is to choose the right kind of batch before you begin. Are you studying one system in many conformations, or processing several different systems with shared simulation settings? The workflows are different, and that distinction affects both preparation and how you choose the periodic box.
One system, many starting conformations
This route is useful when you want each simulation to begin from a different conformation of the same molecular system. Your starting states can be a set of conformations or frames from a trajectory loaded into SAMSON. If the trajectory contains more frames than you want to simulate, you can create conformations for selected frames using the Inspector and Edit > Conformation. Alternatively, create conformations from the path in the Document view, then remove the unwanted ones.
In the GROMACS Wizard’s Prepare tab, set the molecular system, enable [Optional] Batch preparation, and select the conformations or trajectory path. After clicking Set conformations or a path, check the reported number of starting states and use the slider to inspect them. Then continue with the usual preparation choices: force field and solvent, any needed custom index groups, and ions.
The box-size choice is a practical trade-off
For a batch, the periodic box can be based on all conformations or calculated separately for each one. Choose Box lengths when you want the same box size across the batch. The initial size is determined from all selected conformations or the full path; the fitted box may be tight, so increase it as needed to satisfy the minimum image convention.
Choose Solute-box distance when each conformation can have its own box. The documentation recommends at least 1 nm between the solute and the box to help ensure the minimum image convention. This option can give compact conformations smaller boxes, which can reduce computational time. The trade-off is that box sizes will differ between batch members. Use the preparation slider to inspect how the selected box fits the conformations before proceeding.
Several systems, one set of settings
If you are processing different systems—for example, several proteins—prepare each system separately first. Put the resulting -prepare folders together in one batch folder. You can rename the subfolders, such as with PDB identifiers; those names are preserved in later steps. When you start minimization or another subsequent stage, select From batch folder and choose that folder.
One important consistency check: avoid MD parameters that refer to index groups or position restraints specific to only one system in the batch. If a group or restraint record is missing from another member, a shared setup may not be suitable for the whole collection. Review the prepared systems and parameters before launching the next stage.
Run and monitor the batch
Once preparation is complete, the batch project contains separate subprojects. Continue through energy minimization, NVT equilibration, NPT equilibration, and production molecular-dynamics simulation using From batch folder as the input. The auto-fill button can populate the input path from the previous run.
You can launch the jobs locally or in the Cloud. For local runs, a separate job is created for each subfolder and can be managed in the Local jobs window. Cloud runs likewise create a separate job per subfolder, managed through the Cloud jobs window. This makes it possible to track individual members of a batch rather than treating a collection of simulations as one opaque run.
In short: use conformations or trajectory frames when exploring multiple starting states of one system; use a shared batch folder when running separately prepared systems. Think through box consistency and system-specific parameters before launching, and the later simulation stages can follow the same batch-oriented workflow.
For the complete procedure and related steps, learn more in the GROMACS Wizard batch computations tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.