Specifying Initial Conformations in Batch Simulations with GROMACS Wizard

Running molecular dynamics simulations on just one structure rarely tells the whole story. Whether you’re exploring flexible molecules or simulating drug binding in different poses, batch simulations can offer broader insights. But if you’ve ever opened a simulation tool and wondered how to feed in more than one conformation from your trajectory — and do it cleanly — you’re not alone.

In SAMSON’s GROMACS Wizard, batch simulations become straightforward once you understand how to define initial conformations from either a set of conformations or a trajectory path. In this post, let’s zoom into this crucial step — specifying initial conformations when preparing batch simulations. This small but essential step ensures your simulations reflect the structural diversity you’re studying.

When and Why to Use Batch Simulations

Imagine you’re docking a ligand into a protein and you get ten different binding poses. Running a single MD simulation is no longer enough — you want to run one for each pose. Batch simulations help automate this process by treating each pose as a separate input (a subproject). But to do this, GROMACS Wizard needs to know how to treat each conformation in your dataset.

Defining Initial Conformations in GROMACS Wizard

You can start by loading your trajectory into SAMSON. From there, you have two main paths to define initial conformations:

  • Use a Set of Conformations: You can manually or automatically generate a set of static conformations that represent the structures you’re interested in. Each one becomes a starting point for a simulation in your batch.
  • Use a Trajectory Path: If your molecule evolves through time or space, convert your trajectory into a path. Each frame of the path will become a subproject on its own.

To choose either of these, navigate to the Prepare tab and activate the [Optional] Batch project checkbox. Then, depending on your choice, either select the conformations or the path from your document window and click Set conformations or a path.

You’ll then see the number of resulting subprojects and can preview them using a slider:

Choose input type

Creating the Setup

Not happy with the entire trajectory? You can generate specific conformations from selected frames using the Inspector panel:

  • Use Edit > Conformation manually at interesting frames.
  • Or, convert the whole path into conformations using the context menu Path > Create conformations from path. Delete unused ones later.

Benefits of This Workflow

Using conformations or a path makes your batch simulations granular and easy to manage. Each subproject is treated independently and runs in parallel when processed locally or in the cloud. This level of structure ensures simulations are reproducible and manageable, especially when dealing with datasets of growing size.

To learn more and go through the full batch computation pipeline in GROMACS Wizard, visit the original documentation page here: https://documentation.samson-connect.net/tutorials/gromacs-wizard/batch-computations/

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.

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