[gmx-developers] Warnings

hessb at mpip-mainz.mpg.de hessb at mpip-mainz.mpg.de
Sat Aug 9 11:25:33 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.
> 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

Very many people use Berendsen thermo/barostats and for reasonably
large systems this would not affect nearly all properties that
one is interested in. So I don't know if we should warn the user here.
We could add a note that one can use the new v-rescale thermostat
instead of Berendsen to obtain a proper ensemble.

> - tau_t is selected not careful

We could generate a warning when tau_t is <= 10*delta_t.


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