Running molecular dynamics (MD) simulations can be time-consuming, particularly when dealing with multiple molecular conformations or systems. For modelers working with repeated simulations, e.g. for different protein structures or multiple poses of a ligand, having to prepare and simulate each one manually often becomes an efficiency bottleneck.
The GROMACS Wizard in SAMSON offers a convenient solution: batch processing. This is especially useful when performing workflows such as minimization, equilibration, and production MD on a collection of initial conformations or a set of varied molecular systems, all in one go.
Why Batch Simulations Matter
Whether you’re performing ensemble simulations, sampling conformations for umbrella sampling, or benchmarking force fields across protein variants, repeating similar preparation and simulation steps adds overhead.
The batch computation capabilities in the GROMACS Wizard allow you to:
- Automatically prepare multiple simulation setups, each using a different starting conformation or structure.
- Launch all simulations—locally or in the cloud—with consistent parameters.
- Save time by avoiding repetitive manual setup steps.
Using a Set of Conformations
Let’s say you have a single molecular system, but you’ve generated a range of starting conformations, perhaps from a docking trajectory, normal mode analysis, or an animation. You can:
- Load the trajectory into SAMSON by dragging and dropping it or using File > Open.
- Extract specific frames as conformations with:
• Edit > Conformation (to create them manually), or
• Path > Create conformations from path (for a full set). - Go to the GROMACS Wizard’s Prepare tab.
- Check the [Optional] Batch preparation box.
- Select your conformations or trajectory path and click Set conformations or a path.
You’ll know it worked if the conformation count shows up and you can slide through them to inspect.
Periodic Box: Same or Flexible?
One subtle but important option is defining the simulation box. You may choose:
- Box lengths: same box for all conformations (fits to entire set).
- Solute-box distance: box size adjusted per conformation (smaller, more efficient for compact structures).
Tip: Use the slider in the batch preparation interface to see how the box fits each conformation.
From Preparation to Production
Once your batch project is prepared, subsequent steps—minimization, NVT equilibration, NPT equilibration, and production MD—can all be launched for the full batch.
Choose the “From batch folder” input option. Each subfolder (automatically created during batch preparation) will be treated as an independent project, facilitating parallel processing locally or in the cloud.
To monitor progress, use the Local jobs or Cloud jobs windows, depending on where you’re running the simulations.
Saving Time, Reducing Errors
By unifying setup and simulation steps across multiple conformations or systems, batch processing not only saves time but also reduces human error. You can now focus more on analyzing results or designing follow-up experiments—without manually configuring every run.
To learn more, visit the full Batch Computations in GROMACS Wizard tutorial.
*Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.