Saving water in the md.in file.

In this file we implicitly have the default of:
ntwprt = 0
https://github.com/GLYCAM-Web/MD_Utils/blob/stable/protocols/Glycan/NPT_PreMinimized_MD/md.in
Meaning that all waters get written out. Should we explicitly add that flag and then have the scripts figure out and reset it to the correct number to only write out solute? Otherwise our trajectories will be huge by default.

**Here is the amber manual section:**
**ntwprt** The number of atoms to include in trajectory files (mdcrd and mdvel). This flag can be used to decrease the
size of the these files, by including only the first part of the system, which is usually of greater interest (for
instance, one might include only the solute and not the solvent). If ntwprt = 0, all atoms will be included.
= 0 (default) Include all atoms of the system when writing trajectories.
> 0 Include only atoms 1 to ntwprt when writing trajectories.