What next?

• Though you can run simple MD simulations, minimisations and validation with prepmd, for more in-depth MD we recommend using software such as GROMACS, AMBER, NAMD and OpenMM.

• If you’re looking to generate an atomistic structure file that matches your EM map as closely as possible, you can use a flexible fitting tool such as [TEMPy-ReFF](https://gitlab.com/topf-lab/tempy-reff).