David van der Spoel
spoel at xray.bmc.uu.se
Sat Aug 9 11:32:38 CEST 2008
hessb at mpip-mainz.mpg.de 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.
>> - DispCorr = no when using constant temperature. If I understand it
>> 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
>> 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
>> 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.
And the same for tau_p/beta..
Wouldn't it be more useful to supply a few mdp files e.g. on the wiki?
Maybe one for OPLS and one for GROMOS?
As always, the problem is that people would use them without checking
the contents, as people now take the mdp file from the demo and use that
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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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