One of the more subtle challenges in molecular modeling is producing simulated motions that are both physically realistic and computationally efficient. Molecular dynamics can rapidly become inaccurate when atoms move in ways that break the constraints imposed by molecular structures or experimental setups. That’s where constrained simulations step in – and SAMSON provides a flexible toolset for this through the Simulate animation.
If you’ve ever tried to simulate a nanosystem and ended up with a structure behaving in physically implausible ways (for example, atoms flying apart or unrealistic speeds), there’s a good chance constraints weren’t adequately accounted for. In SAMSON, you can combine the Simulate animation with animations that control atom positions to design physically-aware simulations that respect structural constraints.
What is the Simulate Animation?
The Simulate animation performs a multiple-step simulation at each frame of your animation timeline. Think of it as a micro-dynamics engine embedded inside the visual animation tool, seamlessly fusing simulation with representation.
This means you can introduce physics in a controlled way: add the Simulate effect to specific parts of your animation without running a full external molecular dynamics pipeline. This is especially useful when testing designs like molecular machines, protein docking, or nanoscale actuators.
How to Create Constrained Simulations
To simulate constrained behavior:
- Use animations like Record path or Define path animations to dictate specific atom positions or movements.
- Then, insert the Simulate animation below these in the Animator panel so that the simulation starts from these positions.
Ordering matters here. The Animator in SAMSON executes animations from top to bottom, so if you place a Simulate effect before position-defining animations, the simulator won’t know where to begin from. A helpful tip from the documentation: place the Simulate animation after the ones that generate starting positions.
Adjusting Simulation Parameters
Within the Inspector, you can change the number of simulation steps per frame and the step size. This allows you to fine-tune how physically accurate the simulation is. Higher numbers bring more precision but at a cost of performance. Lower values create faster but less detailed motions.
Don’t hesitate to experiment with these values depending on whether your goal is to validate physical plausibility or just illustrate a concept visually.
Example: Speed Matters
In the example below, a nano gripper fails to grasp a nano-cylinder due to excessive approach speed (1.7 nm in 2.5 ps = 680 m/s). Even though everything looked correct visually, the speed exceeded feasible physical limits, and the system failed:
Simulating nanosystems helps designing them. In this example, the actuated part (in blue) of the nano gripper moves down too fast (1.7nm over 2.5ps -> 680m/s) and the gripper fails to grasp the cylinder. (Gripper design by @mooreth42, who showed a successful grasp at a different… pic.twitter.com/M5yKD7uA8T
— Stephane Redon (@StephaneRedon) May 8, 2024
Why This Matters
Accurate simulations are not just important for realism — they influence design decisions. A constrained simulation gives insights into what molecular subsystems may require mechanical dampening, shape changes, or timing adjustments.
More generally, anyone designing nanoscale mechanisms will benefit from running small-scale simulations before committing to full systems. It helps anticipate and fix potential failure points by tweaking inputs and observing outcomes.
Whether you’re testing DNA origami actuators, mechanical proteins, or nanorobots, combining positional control animations and the Simulate effect gives you the means to explore design robustness directly inside SAMSON.
Learn more in the original documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.