On 29/12/10 23:47, Justin A. Lemkul wrote:
I think the root problem boils down to a lack of documentation of this
feature. For most routine use, -maxwarn should not be used, similar to
-missing with pdb2gmx.
Yes, but it depends. In my systems I routinely have to use both to get
the system right, because it's a custom coarse grain and both programs
spit warnings due to quirks of my (surely non-usual) system -that I am
aware of and (as far as I know and I tested) are safe to ignore.
It is your last safeguard when fatal errors
occur, but if it is implied that using it is somehow routine or
convenient, then we begin to undermine the use of all those informative
notes and warnings that grompp prints.
Well, no: grompp should instead print *more* stuff, and explain more in
detail what the warning refers to, showing (for example) the line of the
.mdp or .top file it refers to and stuff like that, and pointing to an
exhaustive manual section to understand it.
This doesn't undermine: quite the opposite, it empowers the user with
*knowledge* that then will use to *decide* what to do.
Looking through the grompp help description, there is no mention of this
feature, and the one-line description is somewhat vague. Perhaps the
best solution is simply to add some documentation, in addition to the
wiki entry I created.
The description of this flag is currently "Number of allowed warnings
during input processing." Perhaps it should say something like "Number
of allowed warnings during input processing. Not for normal use and may
generate unstable systems." I would also think that a description should
be added to the grompp -h text, like:
"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."
If that sounds agreeable, I'll put in an enhancement request.
This makes a lot of sense and I agree in full.
Thanks,
Massimo
--
Massimo Sandal, Ph.D.
http://devicerandom.org
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