Can I use SAMSON to programatically create 20 to 200-mer oligos for simulation (and visualization) of conformational behavior / characteristics (in various temperature ranges)? What is the largest enzyme I can add to the simulation?
You have two ways of programming (e.g. this preparation step) in SAMSON:
Using Python Scripting Element, which allows you to access most of the SAMSON API to process and automatize tasks. See the Python Scripting guide, you can check out tutorials there and the Python Scripting samples.
In the 1st case, you have more functionality and control over processes. The 2nd one is faster to develop and try, and you can further use the developed scripts for your tasks.
For the simulation in which you are interested in, you can use GROMACS Wizard Element (see the GROMACS Wizard tutorial), which allows you to easily run simulations using GROMACS (it comes with the Element) including various temperature ranges. There is yet no possibility to run simulations automatically, but you can launch many simulations in a queue using jobs. In future releases, it will be possible to run them on the cloud. You can freely try this Element for 30-days.
The size of the system for simulation is limited by your computer performance (RAM, CPU, GPU) and the max computation time you are willing to spend. In SAMSON it is possible to load systems with tens of thousands of atoms (depending on the performance of your computer).