Saving water in the md.in file.

[gitoliver]

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.

[Lachele]

I think we need to be able to control that pro grammatically. But, I agree that the default should be solute-only, at least for production.

[Lachele]

@gitoliver - save ions or just the solute by default? Should we allow for control of this?

[gitoliver]

The diffusion calculations will need their own protocol, so we don't care about water here. We don't need control for this now or in the foreseeable future.

I would only save solute. No ions or water. That requires finding out the number of solute atoms in the trajectory and setting ntwprt = that number. We can discuss how to get that number on slack.

[Lachele]

Parm7 file has all the needed info in greppable form. :-)