David van der Spoel
spoel at xray.bmc.uu.se
Fri Aug 8 21:14:40 CEST 2008
Roland Schulz wrote:
> 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.
In some cases you do want more than one group, e.g. when you have
membrane systems there have been cases where there was a net velocity of
the membrane wrt to the solvent (in the lateral direction and also in
the perpendicular direction). Maybe we should investigate the source of
these errors rather than putting up error messages. See e.g.
In general a fat warning is in order I think there is already one for
periodic systems with comm_mode = angular, but people use it nevertheless.
> - DispCorr = no when using constant temperature. If I understand it
> correct this should always be done in that case.
This is more like a force field issue. Some force fields have it, others
> 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)
In general you want protein non-protein if you have this in your
simulation (but sometimes you can have membrane as well). In addition we
should investigate here too why the heat exchange is so bad. This can be
probably be published even. One guy I spoke to many years ago says that
the heat transfer problem is an artifact of the Berendsen thermostat,
but I haven't been able to reproduce that (i.e. I get the same problems
with Nose Hoover).
> - Berendsen: It is not well known that it is not NVT/NPT
> - tau_t is selected not careful
And tau_p should be at least 5 ps in most cases.
These things are definitely at the info level.
> 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.
In order for people to actually read the info, we should probably make
all the other output go away, unless you use the -v option. This is
however quite a bit of work, because this may be in very different
places in the code. I'm not sure we want to do this kind of stuff before
4.0, but you could try to investigate how involved this is, and whether
might break anything.
> Center for Molecular Biophysics ORNL/UT cmb.ornl.gov <http://cmb.ornl.gov>
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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