roland at utk.edu
Mon Aug 11 16:23:04 CEST 2008
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.
Center for Molecular Biophysics ORNL/UT cmb.ornl.gov
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