[gmx-developers] Warnings

[Roland Schulz]

On Sat, Aug 9, 2008 at 5:04 AM, <hessb at mpip-mainz.mpg.de> wrote:

>
>
> >
> > Regarind the thermostat settings I'm not sure whether one should give
> > warnings, messages on a info level or a link to the thermostat wiki page
> > to
> > encourage people to check these parameters.
> > The thinks which are often unclear I think are:
> > - tc_grps: I think often system is used but the wiki page recommends
> > Protein
> > Non-Protein  (for the Hot-Solute Cold-Solvent problem)
> > - Berendsen: It is not well known that it is not NVT/NPT
> > - tau_t is selected not careful
> >
> > I'm happy to do it. Just want to make sure that you agree and I'm not
> > changing the way warnings should work and don't add warnings because of a
> > misunderstand on my side. If you have others to add I can quickly do that
> > too.
> >
> > Roland
>
> We should only generate warnings when we are completely sure that
> certain combinations would not be useful for certain types of systems.
> For "standard" protein in solvent simulations one could probably
> add more checks, but one can simulate any type of system under
> very varying conditions in Gromacs.
> I have already removed several warnings in the past year,
> because some combinations were fine certain cases.


My understanding was, that a warning should be given, when it is very
uncommon choice unlikely to be a good idea. If it is wrong for certain I
thought grompp should give an error.

>
>
> Also one can not check parameter values, since these can vary
> a lot between different systems.
>
> Note that in the new version you already get a fatal error with
> a single warning. This forces people to look at the warnings.
> Also the note count at the end helps people to actually look
> for the notes.
>
> We should add a warning when the comm groups together do not cover
> the whole system. In some cases one might actually want to do this,
> but these are so exotic that a warning is fine.
> When does one get infinity? With multiple groups?
> Or when some atoms do not belong to any group?


It is when atoms do not belong to any group. I'm not sure whether there are
also other cases.

Roland



-- 
Center for Molecular Biophysics ORNL/UT cmb.ornl.gov
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