There are a few programs that run AMBER simulations, and their input files/functionality varies slightly. First, there’s sander (Simulated Annealing with NMR-Derived Energy Restraints). Then there’s pmemd (Particle Mesh Ewald Molecular Dynamics), which builds upon sander. Finally, exists pmemd.cuda, which allows for GPU-acceleration of molecular dynamics (CUDA because it runs on NVIDIA graphics cards. Amazing). Both sander and pmemd are fairly input-compatible, but check the manual before switching between the two.
I’ve most often used pmemd, because the groups I’ve been in tend to run production steps using pmemd.cuda.