Running molecular dynamics simulations on a single system is already a complex task, but what happens when you want to simulate a whole set of conformations? For example, you might have generated different poses from a docking study, explored normal modes to sample motions, or simply want to evaluate stability across key frames from a trajectory. Repeating the simulation setup process for each structure manually can be tedious, time-consuming, and error-prone.
The GROMACS Wizard in SAMSON offers a powerful feature to address this need: batch project preparation. This functionality allows you to automatically prepare and simulate a set of conformations as a batch, saving effort and ensuring consistency across simulations.
Why This Matters
Let’s suppose you’ve docked a ligand into a receptor and generated multiple docking poses. You want to simulate each of these poses to evaluate their dynamic stability or how they interact over time. Instead of preparing each system manually, you can set them all up together and run them through the GROMACS pipeline simultaneously.
Preparing the Batch Project
In SAMSON, generate or load your trajectory or set of conformations using various tools—this could be a sampling animation, a docking path, or a set of structures from other extensions like AutoDock Vina Extended or Normal Modes Analysis.
Then, in the GROMACS Wizard’s Prepare tab, activate the [Optional] Batch project option.
You have two ways to define your initial states:
- Select a set of conformations: Each conformation becomes a subproject in the batch.
- Select a path: Each frame in the path corresponds to a subproject.
Once selected, click Set conformations or a path, verify the number of conformations, and use the included slider to review each one visually.
Defining a Consistent or Flexible Periodic Box
One common challenge when running multiple simulations is deciding whether they should use the same box size or different ones per conformation. GROMACS Wizard offers both:
- Box lengths: Set a single periodic box based on all conformations. Useful when you need consistent boundary conditions.
- Solute-box distance: Tailor the box individually per conformation. This helps reduce computation times for compact structures.
Simulation at Scale
Once your batch is prepared, move on to standard GROMACS steps: Energy Minimization, NVT Equilibration, NPT Equilibration, and Production MD.
For each of these phases, you simply select the batch project as input. The GROMACS Wizard automatically applies the settings to every subproject, ensuring consistency.
If you’re launching simulations locally, each subproject will become a separate local job. These appear in the Local jobs panel, where you can manage them individually: monitor status, reorder, cancel, or open results.
This workflow is ideal for researchers who repeatedly simulate structurally similar systems. Whether you’re running simulations as part of a molecular docking study, conformational sampling, or ensemble-based dynamics—batch project preparation streamlines the process significantly.
To learn more and follow a full step-by-step guide, visit the original GROMACS Wizard documentation on Batch Computations.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.