When preparing molecular dynamics simulations, researchers often work with multiple starting conformations of the same system. This is especially common in studies involving ligand binding, protein flexibility, or comparative dynamics. However, managing and configuring these conformations for batch simulations can be time-consuming and error-prone—unless you’re using tools built for that purpose.
If you’re using the GROMACS Wizard in SAMSON, you can streamline this process by utilizing the batch preparation feature with either a set of conformations or a trajectory path. In this blog post, we’ll walk through how to set up initial conformations for a batch project efficiently—so you can spend less time preparing and more time analyzing results.
Why Initial Conformations Matter
Each conformation can lead to a different outcome in molecular dynamics simulations. For example, the orientation of a ligand in a binding pocket or the starting side-chain rotamers can influence system behavior over time. Running simulations from various initial states lets you explore these possibilities more comprehensively.
Two Ways to Define Initial Conformations in SAMSON
In the GROMACS Wizard’s Prepare tab, you can activate the batch project mode. From there, you have two options for selecting initial states:
- Select a set of conformations: Each conformation becomes an independent starting point.
- Select a path (trajectory): Each frame of the path is used as an initial conformation.
If you already have a trajectory loaded or generated using tools like the Twister, AutoDock Vina Extended, or Protein Path Finder in SAMSON, setting up a path is just a few clicks away. You can also manually define conformations via Edit > Conformation in the Inspector, choosing only the frames of interest.
Batch Preparation Made Simple
After selecting your conformations or path, click Set conformations or a path. You’ll see the number of conformations recognized, and a slider will allow you to preview how each one looks. Toggling through the selected states can help ensure that your system is properly set up before proceeding to box generation and simulations.
This function is especially useful for:
- Saving time by avoiding manual duplication of projects
- Ensuring reproducibility in simulation setup
- Preparing large-scale simulations from docking or normal mode analysis outputs
Flexibility with Periodic Boxes
Once conformations are set, you can also choose how to define periodic boxes. Either:
- Set a shared box size based on all conformations
- Let each conformation have its own box by specifying a solute-box distance (recommended at least 1 nm)
The latter helps optimize computational efficiency for smaller structures without compromising accuracy.
Whether you’re preparing a few simulations or dozens, batch setup with initial conformations in SAMSON’s GROMACS Wizard offers an intuitive, visual way to manage your workflows.
Learn more in the original documentation page: GROMACS Wizard – Batch Computations.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can learn more and download SAMSON at www.samson-connect.net.