In molecular modeling and nanorobotics design, simulations often help uncover hidden flaws before fabrication. One common challenge modelers face is the failure of dynamic nanosystems — for example, a nanogripper missing its target due to faulty motion assumptions.
Let’s explore how you can use the Simulate animation in SAMSON to perform constrained simulations and avoid these frustrations. SAMSON makes it easier to coordinate movements and forces in nanosystems by allowing animations to interact together. This is especially useful when trying to understand component behavior under specific controlled constraints.
Simulate with Precision
The Simulate animation in SAMSON performs a multiple-step simulation at each animation frame. It can be inserted in the Animator panel to let you continuously simulate the dynamics of your molecular system. But what makes it especially effective for precision tasks, such as nanogripper operation, is its ability to be combined with other animations that control atomic positions.
Let’s say you have an actuator designed to close two nanoscale arms around a cylindrical object. If you simulate this actuation without accounting for realistic physical feedback (for example, inertial effects or constraints from surrounding atoms), the simulated arms might overshoot the cylinder — or miss it entirely — as shown in the following example:
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
Integrating Constrained Motions
To resolve issues like this, you can combine Simulate with other animations such as Set Position or Displacement to define a coordinated, physically realistic motion path for each part of the nanostructure.
For example, you can:
- Add the Simulate animation by double-clicking it in the Animation panel.
- Place it after other animations in the stack that define starting positions. SAMSON executes animations top-down, so simulation effects should come after positional/fixed movements.
- Adjust the number of steps per frame and the step size via the Inspector panel, to control the resolution and speed of your simulation.
This workflow lets you include inertia and portioned interactions into simulated trajectories. The example above shows what can go wrong if the setup lacks constraints — the arms moved at 680 m/s and failed their task within 2.5 ps. Repeating the simulation with restricted motion and realistic force modeling can lead to success.
Refining Your Results
Once you’re happy with a constrained simulation, you can record it using the Record path animation, then play it back smoothly using Play path or in reverse with Play reverse path. This opens up a workflow for iteratively testing, comparing, and refining nanosystem designs.
Want to try this workflow for yourself? Explore the full documentation on the Simulate animation page for step-by-step instructions and examples.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.