Designing molecular systems in motion can be tricky. A frequent challenge molecular modelers face is controlling atom positions while running simulations—especially when certain parts of a nanosystem are meant to stay fixed or move in a strictly defined way.
If you’ve ever wished to run simulations while constraining atom movements—like limiting the flex of a hinge in a molecular machine or ensuring a ligand follows a specific binding path—then constrained simulations are what you’re after.
In SAMSON, constrained simulations can be achieved by cleverly combining the Simulate animation with other animations that dictate the motion or position of atoms. This creates a powerful workflow where control and dynamics come together seamlessly.
Combining Animations for Constrained Motion
The basic idea is simple: stack animations in the Animator panel in a specific order. Here’s how it works:
- Start by adding animations that position or displace atoms along predefined paths or according to certain rules.
- Then add the Simulate animation underneath them in the Animator.
SAMSON executes animations from the top down. That means the Simulate animation will see the atom positions already determined by the previous animations and apply dynamics on top of them. The result? A constrained simulation where atom movement is partially controlled and partially governed by physics.
Why This Matters
Running constrained simulations like this allows modelers to experiment with partial flexibility, apply guided dynamics to flexible linkers, or preserve specific system configurations.
For example, consider a nanoscale gripper arm attempting to grasp a cylinder. You can guide the arm with a positioning animation and then combine that with a simulation that models realistic interactions. Adjusting the simulation step size or the number of steps per frame allows you to fine-tune the dynamic response while maintaining your predefined motion control.
Getting Started
To set it up:
- Open the Animator panel in SAMSON.
- Double-click to add your control animation (like Record path or a motion animation).
- Then double-click on Simulate to add it below the control animation. It will be added at the current frame—move the keyframe if needed.
- In the Inspector, tweak parameters like the number of steps per frame or the step size to adjust simulation precision.
This technique is particularly useful when designing molecular machines, probing stability under partial constraints, or even modeling nano-mechanical parts with guided input.
To learn more and see examples, check the full documentation page on the Simulate animation in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.