roland at utk.edu
Fri Aug 8 20:55:51 CEST 2008
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
- 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
Center for Molecular Biophysics ORNL/UT cmb.ornl.gov
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-developers