Molecular Dynamics

Figure 1: The protein adenylate kinase (AdK) undergoes a structural change during its catalytic cycle between a closed and an open state that is captured in enhanced sampling simulations (Seyler et al. 2015). The protein secondary structure is shown as a round ribbon with individual amino acid sidechains as ball-and-sticks. The trajectory was rendered with Blender and the MolecularNodes plugin (Brady Johnston). Trajectory files are available via MDAnalysisData Copyright CC-BY 2023 Brady Johnston.

As well as importing static structures, the results from molecular dynamics simulations can be imported as models in to Blender. This is enabled through the excellent package MDAnalysis. The imported structure will have an object created that will act as the topology file. Depending on the import method, the frames of the trajectory will either be streamed from the disk, or loaded in to memory inside of the .blend file as their own separate objects.

MD Trajectory Panel

To import trajectories, change the import method in the Molecular Nodes panel to the MD method.

The minimum requirements are a valid `Topology`` file, that can be read by MDAnalysis.

If just a topology is selected then a static model should be imported. If additionally a trajectory is selected, then the toplogy will have coordinates that change when the Frame changes inside of Blender.

Below selects some example MDAnlaysis data for import, without changing any of the defaults.

Import Options

Before importing, we can change some of the import settings to be applied on import. More detail on each option is further in this tutorial, but the short descriptions:

• Style Tick box whether to set up nodes to apply a style, or just import the data. If enabled, a default style to be applied on import is selected. This can be changed easily after import.
• Import Filter a MDAnalysis selection string to filter the topology when importing. Default is to import everything, but you can input strings such as ‘protein’ to only import the protein component.
• In Memory Whether to load the selected frames (from start to stop, incrementing by step) into memory and discard the MDAnalysis session when importing. Default is false and streams the trajectory from disk.
• Custom Selections Users can create multiple custom selections that appear as boolean attributes on the imported trajectory. Useful for creating groups using MDAnalysis selection strings to then utilise inside of the created node tree.

Import the Trajectory

Click Load to import the selected trajectory with the chosen options. The model will appear in the scene, and once you change frame in the scene, it will update the frame displayed in the viewport.

Changing Style

You can change the style by altering the Style nodes that are use inside of the node tree.

As you can see in the example, if we don’t apply the style, we can view just the raw atomic data that is being updated. Depending on which nodes we use to process that data, we can create different styles of further animations.

Subframes

By default, each frame on the timeline matches directly with the frames in the loaded trajectory.

You can add subframes which then tell Blender to add additional frames in between, which linearly interpolate between positions. This can slow down the animation and sometimes make it easier to view. The subframes for the trajectory can be adjusted in the Object section of the Molecular Nodes panel.

The Frame number in Blender no longer directly matches the frame displayed from the trajectory, with the trajectory playing back ‘slower’ than previously.

Streaming vs In Memory

Streaming

The default option will associate an MDAnlaysis session with the read topology file. This will stream the topology from disk, as the frame in the scene inside of Blender changes. If the original topology or trajectory files are moved, this will break the connection to the data. This is the most performant option, but will potentially break if changing computers.

Below is an example of importing a trajectory, by streaming the frames. As the frame changes in the scene, the loaded frame is updated on the imported protein, based on the created MDAnalysis session. Interpolation between frames is currently not supported with this import method.

The MDAnalysis session will be saved when the .blend file is saved, and should be restored when the .blend file is reopened.

In Memory

The In Memory option will load all frames of the trajectory in to memory, and store them as objects inside of the MN_data collection in the scene. This will ensure that all of the associated data is stored inside of the .blend file for portability, but will come at the cost of performance for very large trajectories. It also breaks the connection to the underlying MDAnalysis session, which limits the ability to further tweak the trajectory after import.

If In Memory is selected, the frames are imported as individual objects and stored in a MN_data collection. The interpolation between frames is then handled by nodes inside of Geometry Nodes, which aren’t necessarily linked to the scene frame.

This will create a larger .blend file and can lead to some performance drops with large trajectories, but ensures all of the data is kept within the saved file, and can enable further creative control through Geometry Nodes.

All connection to the underlying MDAnalysis session is lost on import, and the selections and trajectory cannot changed. To make changes you must reimport the trajectory.

Creating the Animation

To replicate the animation which we see at the top of the tutorial, we can use some of the example datasets which are provided alongside MDAnalysis with the MDAnalysisData package. To download one of the datasets, use the code below:

# pip install MDAnalysisData
from MDAnalysisData import datasets
datasets.fetch_adk_transitions_FRODA()

Loading the Trajectory

We will load the trajectory, and load all of the frame sin to memory to ensure we can make a smoother trajectory.

In the video below we have imported the trajectory, and we can adjust the number of frames in the scene, as well as the number of frames the trajectory will play back over. We also enabled EEVEE atoms to display in the EEVEE render engine.

Changing Styles

We can change the style of the imported trajectory, by adding a new style node. We can combine styles with the Join Geometry. For more details on adding styles, see the (importing)[01_importing.qmd] tutorial.

We can apply the atoms style, only to the side chains of the protein, by using the Backbone selection node, and using the is_side_chain output. This selectively applies the style to only those atoms in the selection. The combined styles now contain only the atoms for the side chains and a continuous ribbon for the protein.

Setting the Scene

We can set up the scene a bit nicer with a backdrop. In this case we create a plane using Shift + A to add a plane, go in to edit mode and extrude the backbdrop up with the E key. We can create a slightly curved corner by bevelling the corner. Select the two vertices of the edge and click Ctrl + B. Move the mouse and use the scroll wheel to adjust the settings, then left click to apply.

Rendering the Animation

We can change some final settings of the style, do a test Render Image, change the export settings for where the frames of the animation are going to be saved, then we can click Render Animation to render all of the frames of the animation.

References

Seyler, Sean L., Avishek Kumar, M. F. Thorpe, and Oliver Beckstein. 2015. “Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways.” Edited by Emad Tajkhorshid. PLOS Computational Biology 11 (10): e1004568. https://doi.org/10.1371/journal.pcbi.1004568.