For molecular modelers running multiple simulations on variants of the same system—perhaps different conformations, docking poses, or even frames of an animation—preparing separate GROMACS input files manually can become repetitive and time-consuming. If you’ve been through the cycle of setting up the same simulation steps over and over with slight differences, there’s good news: SAMSON’s GROMACS Wizard includes a batch project feature to automate this preparation.
This is especially useful when dealing with a trajectory or a path of molecular conformations. For example, you might want to simulate several docking poses obtained from AutoDock Vina Extended, or slices of a movement path from molecular animations.
Batch Project Setup: How It Works
In SAMSON, a batch project consists of a set of subprojects, each corresponding to one conformation or one frame. Here’s how to make it work for you:
1. Selecting Input Structures
You can choose between two options:
- A set of conformations: Each one will become its own subproject.
- A path (trajectory): Each frame will become a subproject.
To do this, select the conformations or path directly in your SAMSON Document view, then click Set conformations or a path. You’ll see a number indicating how many subprojects will be prepared.
2. Prepare Once, Apply to All
Once input structures are selected, go to the Prepare tab in the GROMACS Wizard and activate the [Optional] Batch project checkbox. From here, you can continue following the usual steps:
- Choose the model: Force field and solvent settings are common across subprojects.
- Set the molecular system: Choose the relevant structure from your document.
- Add index groups: Custom groups can be included for later restraint or analysis.
- Define the periodic box: Either fitting all structures together or calculating individual boxes based on solute-box distance.
3. Batch-Specific Box Configuration
One advantage of batch setup is flexible box sizing. You can choose either:
- Unified box: Based on all conformations or path frames.
- Per conformation: Distinct boxes calculated per structure (recommended minimum solute-box distance: 1 nm).
4. Preview and Adjust
Use the slider in the Batch preparation section to preview how your simulation box fits each conformation. This helps catch issues early and fine-tune box size or positioning.
5. Streamlined Simulation Setup
After batch preparation, proceed with minimization, equilibration, and production the same way as with single projects. Choose the batch folder as input, and you can compute locally or in the Cloud. When running locally, each subproject will appear as an independent job in the Local Jobs window, giving you monitoring and control options.
Why This Matters
Instead of repeating steps for each structure, batch preparation centralizes the workflow, reduces errors, and saves time. This is particularly advantageous when comparing simulation outputs for docking variants, conformational stability, or experimentally derived frames.
Learn more in the GROMACS Wizard documentation on batch computations here: https://documentation.samson-connect.net/tutorials/gromacs-wizard/batch-computations/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.