Yes. You can. The entire program was built and was functional on CPUs well
before GPUs came into the picture. Due to the way calculations are
off-loaded to GPUs not all features available on CPUs are available in the
GPU implementation. cutoff-scheme = Verlet is one such example. For more
details
If you want a simulation w/o Zinc as a control then build a new system/pdb
w/o it (just delete the Zn line) rather than doing something exotic like
turning off its charge. Turning off charges (and van der Waals parameters)
is an approach more suitable for alchemical calculations
