If you work in molecular modeling, you’ve likely faced the challenge of simulating multiple states or conformations of the same molecular system. Maybe you generated a trajectory from a docking animation, or you explored conformational changes using normal mode analysis. Either way, running separate simulations for each frame or state can quickly become repetitive and error-prone.
The GROMACS Wizard in SAMSON offers a structured solution to this problem with its batch computation project feature. This approach allows you to define a whole set of initial conformations—either as individual states or trajectory frames—and automatically set up separate simulation projects for each. Let’s walk through how you can leverage this in practice.
Why batch processing helps
Let’s say you’ve got ten docked conformations of a ligand bound to a receptor. You want to run molecular dynamics (MD) simulations on all of them to assess stability. Instead of setting up ten separate projects manually, the GROMACS Wizard lets you:
- Select the conformations or a trajectory path
- Create a batch project with one simulation subfolder per conformation
- Run them all together—either locally or in the SAMSON Cloud
Setting it up
To get started, first create or import your conformations into a SAMSON document. You can do this from animations, docking results, or other modeling tools. If you need only specific conformations from a trajectory, use the Edit > Conformation menu while navigating frames to create a tailored set.
Once ready, open the Prepare tab in the GROMACS Wizard and toggle the [Optional] Batch project box. You’ll then be prompted to set either a path or a set of conformations as your input. A convenient slider lets you browse the selected conformations, giving you full control over what’s included.
Customizing preparation steps
The wizard helps you walk through key setup choices:
- Force field and solvent selection: Set the molecular model appropriately
- Index groups: Add custom groups for later use in analysis
- Periodic box definition: You can either apply the same box to all conformations or tailor a box per frame using solute-box distance (recommended >= 1 nm)
Running the simulations
After preparation, follow the normal simulation pipeline—energy minimization, equilibration (NVT, NPT), and production MD—for the batch project just like you would for a single one. Use the Auto-fill button to set paths consistently across steps.
When you launch simulations locally, each subproject runs as a separate job and is listed in the Local jobs panel. You can monitor, reorder, and manage them independently. Alternatively, upload to the Cloud to run multiple simulations in parallel without tying up your machine.
When to use it
Batch simulation workflows are particularly useful if you:
- Dock multiple ligands or poses and want comparative dynamics studies
- Generate conformational ensembles through normal mode sampling, path planning, or manual editing
- Need to capture the effect of conformational variability on MD outcomes
The batch project system removes the redundancy from repeating simulation setup and keeps your workflow consistent and easier to reproduce.
To learn more, visit the original documentation page: https://documentation.samson-connect.net/tutorials/gromacs-wizard/batch-computations/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.