Improving grompp documentation
Per the discussion on the users' list (http://lists.gromacs.org/pipermail/gmx-users/2010-December/057140.html), I would suggest that the help information generated by grompp be amended to prevent users from casually employing -maxwarn when they shouldn't. Proposed changes:
1. Additional information in the one-line summary of the -maxwarn option. Presently it says "Number of allowed warnings during input processing." I would suggest it be amended to say "Number of allowed
warnings during input processing. Not for normal use and may generate unstable systems."
2. Adding mention of -maxwarn in the -h output, i.e. "The -maxwarn option can be used to override warnings printed by grompp that otherwise halt output. In some cases, warnings are harmless, but usually are not. The user is advised to carefully interpret the output messages before attempting to bypass them with this option."