Running molecular dynamics (MD) simulations across multiple systems can be one of the most time-consuming bottlenecks in molecular modeling. If you’ve ever found yourself repeating the same preparation and simulation steps manually for dozens of protein-ligand systems, you likely know how tedious and error-prone the process can become.
Fortunately, the GROMACS Wizard in SAMSON offers a convenient solution for handling these workflows at scale. Whether you’re testing the same simulation protocol across different proteins, or analyzing how multiple ligands affect a target structure, you can automate the process using the batch computation capabilities.
Why batching matters
Batch processing isn’t just about convenience—it reduces frustration, minimizes repetitive errors, and increases reproducibility. By performing preparation, minimization, equilibration, and production simulations on multiple molecular systems in a consistent manner, you ensure that your comparisons are fair, your workflows are replicable, and your notebook is less likely to be filled with repeated commands.
Preparing multiple systems in a single batch
Here’s how you can efficiently set up a molecular dynamics workflow on a set of different molecular systems in SAMSON:
- Prepare each system individually using GROMACS Wizard’s Preparation step. Each processed system is saved in a folder ending with
-prepare. - Group all these
-preparefolders into one overarching folder (you can rename them for easier tracking). - For the next steps (minimization, equilibration, production MD), select “From batch folder” as your input source and specify the batch folder.
Batch simulations: local or in the cloud
Once your batch project is structured, you can run the simulations either locally or in the Cloud:
- Local jobs: Each subproject is launched as an independent local job. You can monitor progress in the Local jobs window and stop or reprioritize as needed.
- Cloud jobs: Each system is uploaded as a separate Cloud job, which you can manage through the Cloud jobs interface.
Things to keep in mind
- Ensure that your MD parameters don’t include index groups or POSRES records unique to only one system—these might not exist in others, causing errors.
- The batch folder structure is preserved throughout, so you can keep track of each system by its name or identifier.
This workflow is ideal for virtual screening follow-ups, comparing structural variability across homologs, or running perturbation experiments across multiple conformers.
To learn more and access step-by-step instructions with examples, see the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.