ms wrote:
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 sounds very much like your systems are in the minority - those for which
-maxwarn is essential :)
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.
What I meant was that -maxwarn allows a user to casually bypass that which
grompp is already printing, something that has caused problems at least 2 or 3
times now in the last week, I believe.
I know of at least one commonly-used tutorial supplies example grompp commands
with -maxwarn and no explanation as to what it's doing or why it's being
invoked. What we need to do is avoid this blind practice. I think grompp has a
sufficient level of verbosity for most cases. In most (if not all) instances,
the lines in the .mdp and/or .top are clearly indicated.
<snip>
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.
Great, thanks.
-Justin
Thanks,
Massimo
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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