hessb at mpip-mainz.mpg.de
Mon Aug 11 16:54:49 CEST 2008
Roland Schulz wrote:
> On Sat, Aug 9, 2008 at 5:04 AM, <hessb at mpip-mainz.mpg.de
> <mailto:hessb at mpip-mainz.mpg.de>> wrote:
> > Regarind the thermostat settings I'm not sure whether one should
> > 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.
But is should be very uncommon for any type of system.
For example, many people are now also using Gromacs for coarse grained
Here one my be using sigma-epsilon units which makes any absolute value
I think David's idea of providing proper example md files is a better
way of helping
people avoid stupid mistakes. Now people just copy mdp files from a
> 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.
I have fixed this problem a few months ago.
Or is there still a problem like that present in the current CVS?
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