This extension contains a set of state updaters.

State updaters are used in SAMSON to update the state of a dynamical model. They may be used for simulation or minimization.

The six state updaters included in this SAMSON Element are:

• adaptive steepest descent (adaptive minimization),
• adaptively restrained NVE (symplectic adaptively restrained dynamics simulation in the NVE ensemble),
• interactive modeling updater (adaptive minimization with displacement constraints for stable edition),
• partitioned Euler (a classical symplectic integrator),
• steepest descent (a classical minimization method),
• velocity Verlet (a classical symplectic integrator).

Use the adaptively restrained NVE integrator to control the tradeoff between precision and computational cost when performing constant-energy simulations.

Usage

To add an interactive simulator to the document:

• Select what you want to simulate. If nothing is selected, all atoms in the document will be simulated.
• In the Edit menu, click "Add simulator". Alternatively, press Ctrl / Cmd + Shift + M.
• Select an interaction model (force field)
• Select a state updater
• Click OK
• Click Start to start the simulation (or press X).

See also

User Guide: Modeling and Simulation