Running the same molecular-dynamics workflow on many starting structures can become a project-management task of its own. Repeating setup by hand makes it harder to keep parameters consistent, and it takes time away from interpreting results. GROMACS Wizard batch computations help organize this work by preparing multiple subprojects that can proceed through the workflow together.
The first decision is what you are batching: many conformations of one molecular system, or several different systems. These cases have different setup requirements, and choosing the right route makes the rest of the process easier to reason about.
One system, many starting conformations
This route is useful when you want to apply the same workflow to multiple states of the same system—for example, selected frames from a trajectory. In SAMSON, you can open a trajectory or create conformations using available tools and extensions. If only particular frames are needed, create conformations from those frames in the Inspector. Alternatively, create conformations from the whole path and remove the ones you do not need.
In the GROMACS Wizard Prepare tab, set the molecular system, enable Batch preparation, and select either a set of conformations or a trajectory path. Each selected conformation—or each frame in the path—becomes the starting state for a subproject. The Wizard lets you check the number of selected conformations and preview them with a slider before preparing the batch.
That preview is worth using: it is a simple opportunity to confirm that the intended states were selected before generating a collection of projects. Then choose the force field and solvent, specify ions, and add custom index groups if they will be useful later for analysis or simulation.
Choose box behavior deliberately
For conformational batches, the periodic box can be defined in two ways. Box lengths sets a common box based on all conformations or the full trajectory. This is useful when identical box dimensions across the batch matter. A tightly fitted box may need to be enlarged to satisfy the minimum image convention.
Solute-box distance instead defines the distance between the solute and the box for each conformation. The resulting box sizes can vary across the batch. The documentation recommends at least 1 nm to help ensure the minimum image convention. If some conformations are more compact than others, this option can avoid using a larger common box for every state and may reduce computational time. Use the preview slider to inspect how the chosen box fits the different conformations.
Several different systems
If the batch contains different systems, prepare each one separately first. Put the resulting folders ending in -prepare into a shared batch folder. You can keep their existing names or rename them—for example, using PDB identifiers—and those subfolder names are preserved in later steps.
A key consistency check is needed here: avoid MD parameters that refer to index groups or position restraints that exist in one system but not the others. Such system-specific settings can make a shared batch workflow unsuitable for the full set. Review the prepared systems and shared parameters before launching the batch.
Run, monitor, and keep the projects organized
After preparation, the standard sequence remains the same: energy minimization, NVT equilibration, NPT equilibration, and production molecular-dynamics simulation. At each step, select From batch folder as the input. The auto-fill button can populate the path based on the previous run.
Each subfolder is a separate project. When computations are launched locally, the batch creates a separate local job for each subfolder. Cloud runs similarly create one Cloud job per subfolder. The Local jobs and Cloud jobs windows let you monitor status and manage the jobs, including actions such as stopping or canceling; Cloud jobs can also be downloaded and imported. Thinking of the batch as a collection of independent projects helps when checking progress or identifying which system needs attention.
For the full procedure and related setup details, see the GROMACS Wizard batch computations tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.