[gmx-developers] Warnings

hessb at mpip-mainz.mpg.de hessb at mpip-mainz.mpg.de
Sat Aug 9 11:04:25 CEST 2008

> Hi,
> I recently saw some questionable grompp parameters and was wondering what
> you think about adding some more Warning messages to grompp.
> At the moment I could think of the following cases:
> - comm_grps not none or System. I can't think about a reason were it makes
> sense and certainly in most cases you don't want to do that. Also the code
> in readdir.c doesn't work correctly in that case. It doesn't compute the
> degrees of freedoms for these groups and then you get an error message
> saying vcm temp is inifinite.
> - DispCorr = no when using constant temperature. If I understand it
> correct
> this should always be done in that case.

DispCorr has nothing to do with temperature coupling.

> 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.

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?
This should be fixed.


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