When setting up molecular dynamics simulations for a series of molecular conformations, choosing the right periodic box parameters can lead to more efficient simulations and better results. In SAMSON’s GROMACS Wizard, users working with multiple conformations have two main options when it comes to defining a periodic simulation box for a batch project.
This post focuses on helping you decide which periodic box method best suits your modeling needs when working in batch mode.
Why the Periodic Box Matters
The periodic box is the boundary that defines the simulation space. Its size and shape can have a direct impact on simulation time, the accuracy of interactions, and the validity of results under periodic boundary conditions. For batch simulations, where each conformation represents a different starting condition, the choice of box setup becomes even more important.
Two Strategies, One Goal
In the Prepare tab of the GROMACS Wizard, when enabling batch mode, you need to choose how to define the periodic box for your simulation:
1. Box Based on All Conformations
In this method, the box is designed to fit all conformations or frames in the batch. You manually define the box lengths. During fitting, the system is placed inside the box, and you can shift the placement to center it. This ensures that every conformation runs inside the same box, which can simplify post-processing and comparisons — very useful when conformations are similar in size and shape.
Pros:
- Simplified setup and analysis
- Uniform simulation space
Cons:
- Can waste computational resources if some conformations are more compact
2. Box Per Conformation Using Solute-Box Distance
This approach lets you define a minimum distance between each molecular system and box edge (typically at least 1 nm). The result: each conformation gets its own box adjusted to its size. More compact systems result in smaller boxes—and faster simulations.
Pros:
- Minimized simulation box volume per conformation
- Better computational efficiency
Cons:
- Results in varying box sizes, which can complicate post-simulation data comparisons
When to Use Which?
If you are modeling a relatively rigid system (e.g., comparing slightly different ligand poses), using the same box for all runs via the first method is ideal. On the other hand, if your conformations differ significantly in size—such as during unfolding simulations—it’s better to switch to defining individual boxes based on solute-box distances.
To visualize how the periodic box fits your conformations, use the slider in the Batch preparation section after box setup. This helps avoid box-system overlaps or unnecessarily large solvent volumes.
Conclusion
Efficient simulations start with informed decisions. By understanding the trade-offs between uniform and per-conformation periodic box strategies, you can reduce computational time and simplify analysis workflows. Take a moment to review your system’s diversity and choose the approach that aligns with your goals.
To learn more about batch simulations in GROMACS Wizard for SAMSON, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.