Production protocol for globular and membrane proteins
It also includes a possible flatbottom potential box
Number of steps to run the simulations in units of 4fs
Temperature of the thermostat in Kelvin
Force constant of the flatbottom potential in kcal/mol/A^2. E.g. 5
Reference selection to use as dynamic center of the flatbottom box.
Selection of atoms to apply the flatbottom potential
Position of the flatbottom box in term of the reference center given as [xmin, xmax, ymin, ymax, zmin, zmax]