A molecular mechanism can look convincing in a static view and still fail when it moves. One common reason is that an actuated part is driven too quickly: the surrounding atoms may not have enough simulated time to respond as intended. The result can be a missed contact or a failed grasp, even when the starting geometry appears right.
The Simulate animation in SAMSON helps you examine what happens during motion. It performs multiple simulation steps at each animation frame, so you can combine it with animations that control atom positions and observe how the modeled system responds.
Use motion and simulation together
For a constrained simulation, first use an animation to generate the starting positions or drive the part you want to move. Then place the Simulate animation after it in the Animator. This order matters: the Animator executes animations from top to bottom, so the simulation should follow the animation that establishes the positions for that frame.
To add it, double-click Simulate in the Animation panel. Its keyframe is placed at the current frame, and you can move that keyframe if the simulation should begin elsewhere in the animation. Keyframes can be repositioned later, which makes it easier to adjust the sequence as you refine the motion.
Read the motion in context
Consider the documented nano-gripper example. Its actuated blue part moves down by 1.7 nm over 2.5 ps, corresponding to a speed of 680 m/s. At that speed, the gripper fails to grasp the cylinder. The useful lesson is not simply that a particular speed is always wrong; it is that a designed movement needs to be assessed alongside the response of the rest of the molecular system.
When a grasp or contact fails, inspect the timing of the imposed movement as well as the geometry. Ask whether the moving component reaches the intended position too quickly for the modeled system to respond. Simulation gives you a way to examine the evolving structure rather than judging only the initial and final poses. Treat the result as a diagnostic of the setup and motion, not as a substitute for checking whether the model and simulation conditions are appropriate for your question.
Adjust the simulation granularity
The Simulate animation’s Inspector lets you change the number of simulation steps per frame and the step size for the simulator’s state updater. These are the controls to review when you need to adjust how the simulation advances during the animation. Change them deliberately and compare the resulting trajectories; the documentation does not prescribe one universal setting, because the appropriate choice depends on the system and the purpose of the simulation.
A practical workflow is to establish the driven motion, place Simulate after it in the Animator, and inspect whether the system achieves the intended interaction. If the trajectory is important for later review or comparison, add the Record path animation to save it. You can also explore the related Play path and Play reverse path animations.
For setup details, see the Simulate animation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.