If you’ve ever attempted to animate a nanosystem and simulate molecular movement—only to discover, too late, that your design fails at a key moment—you know the frustration. Perhaps your nano gripper misses its target, or its moving part flies off uncontrollably. This can happen when molecules move too fast or in undesired directions due to poorly constrained simulations. Fortunately, there’s a way to anticipate these failures before they happen: constrained simulations using the Simulate animation in SAMSON.
Constrained simulations can help you test design ideas early by combining physics-based simulation with controlled atomic motion. This means you can simulate how your nanosystem behaves given a set of intended movements.
What is a constrained simulation?
In SAMSON, the Simulate animation performs a multi-step simulation at each animation frame. By itself, this provides a way to visualize dynamic behavior. But SAMSON becomes especially powerful when you combine Simulate with other animations that control atomic positions. For instance, if you use a motion path or input specific motions for certain atoms, the simulation will respect those as constraints while still applying force-field-based interactions under the hood.
Let’s say you want to check whether a nano gripper properly grabs a molecule when one arm moves downward. Instead of waiting until fabrication to see if the gripper fails (which is costly and time-consuming), you can set up the arm’s motion path and run a constrained simulation. SAMSON will simulate the system’s response—including fast motions that might otherwise ruin the grip.
Examples from practice
Here’s a real-world example from the SAMSON team, showing a nano gripper whose actuated blue part moves too fast: 1.7 nm in just 2.5 ps, leading to a speed of 680 m/s. The system fails to grasp the cylinder due to this overly fast motion.
This would have been hard to detect using static structures or linear interpolation alone. By performing a constrained simulation, however, the issue becomes visible almost immediately.
How to get started
To try it out in SAMSON:
- Go to the Animation panel and double-click on Simulate. This adds a keyframe at the current animation frame.
- Make sure this comes after any position-based animations—for example, a path that moves a specific atom—as SAMSON executes animations from top to bottom.
- If needed, adjust the position of the keyframe by dragging it along the animation timeline.
- Inspect and change the number of simulation steps per frame and the step size using the Inspector.
Why this matters
Simulating designed motion with atomistic interactions helps you detect design flaws early. Whether you are designing a nanoscale actuator, a drug-target interaction, or a mechanical gesture at the molecular scale, constrained simulations give you greater confidence in motion planning.
Try it next time you’re animating a functional molecular system, and see how it changes your design process.
To learn more, visit the full documentation page here: https://documentation.samson-connect.net/users/latest/animations/simulate/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.