Running molecular dynamics simulations across a large number of protein structures—whether they are variants, mutants, or alternative binding poses—can quickly become overwhelming. Repeating the same MD preparation steps for each conformation or each structure wastes time, increases chances of human error, and drains focus from the science.
The GROMACS Wizard in SAMSON offers a clean solution: batch projects. In this blog post, we’ll look specifically at how to run energy minimization, equilibration, and simulation in batch, after preparing these systems beforehand. This setup not only reduces effort but ensures consistency across all simulations, making your results more reliable and reproducible.
Ready, Set, Simulate
Once your batch project is created (you may follow the preparations for a set of conformations or different systems), you’re set for the next steps. The GROMACS Wizard allows you to execute the full spectrum of simulations—Energy Minimization, NVT Equilibration, NPT Equilibration, and Production MD—on all systems in your batch with only a few clicks.
In each simulation step, simply select “From batch folder” as the input. That’s where SAMSON looks for the prepared subfolders you previously created for each conformation or system. You can even use the auto-fill button to automatically carry over paths used in the previous simulation stage, which helps avoid mistakes and speeds up the workflow.
Running Locally or in the Cloud
You can choose to run the simulations locally or in the cloud, depending on your resources. Locally, each subproject is treated as a separate job and appears in the Local jobs window. From there, you can:
- Monitor job progress
- Change job priorities
- Cancel jobs
- Re-import or open result files
If you need access to more computational power, cloud computing is also supported. Each subproject becomes a separate job on the cloud, also fully manageable from SAMSON’s Cloud jobs window.
Useful Notes
When running batch simulations across different systems, make sure your MD parameters are general enough. Don’t use index groups or position restraints defined for a particular structure that’s not present in others. This prevents simulation failures due to missing dependencies.
This feature is very handy when comparing the dynamics of multiple ligand-bound states, simulating protein homologs under the same conditions, or sampling multiple conformations identified in docking or normal mode analysis. You prepare once and simulate them all together with consistent simulation parameters.
Learn more about batch simulations in the official documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON here.