<div dir="ltr"><br><br><div class="gmail_quote">On Sat, Aug 9, 2008 at 5:04 AM, <span dir="ltr"><<a href="mailto:hessb@mpip-mainz.mpg.de">hessb@mpip-mainz.mpg.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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<div class="Ih2E3d"><br>
><br>
> Regarind the thermostat settings I'm not sure whether one should give<br>
> warnings, messages on a info level or a link to the thermostat wiki page<br>
> to<br>
> encourage people to check these parameters.<br>
> The thinks which are often unclear I think are:<br>
> - tc_grps: I think often system is used but the wiki page recommends<br>
> Protein<br>
> Non-Protein (for the Hot-Solute Cold-Solvent problem)<br>
> - Berendsen: It is not well known that it is not NVT/NPT<br>
> - tau_t is selected not careful<br>
><br>
> I'm happy to do it. Just want to make sure that you agree and I'm not<br>
> changing the way warnings should work and don't add warnings because of a<br>
> misunderstand on my side. If you have others to add I can quickly do that<br>
> too.<br>
><br>
> Roland<br>
<br>
</div>We should only generate warnings when we are completely sure that<br>
certain combinations would not be useful for certain types of systems.<br>
For "standard" protein in solvent simulations one could probably<br>
add more checks, but one can simulate any type of system under<br>
very varying conditions in Gromacs.<br>
I have already removed several warnings in the past year,<br>
because some combinations were fine certain cases.</blockquote><div><br>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. <br>
</div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
<br>
Also one can not check parameter values, since these can vary<br>
a lot between different systems.<br>
<br>
Note that in the new version you already get a fatal error with<br>
a single warning. This forces people to look at the warnings.<br>
Also the note count at the end helps people to actually look<br>
for the notes.<br>
<br>
We should add a warning when the comm groups together do not cover<br>
the whole system. In some cases one might actually want to do this,<br>
but these are so exotic that a warning is fine.<br>
When does one get infinity? With multiple groups?<br>
Or when some atoms do not belong to any group?</blockquote><div><br>It is when atoms do not belong to any group. I'm not sure whether there are also other cases.<br><br>Roland <br></div></div><br><br clear="all"><br>
-- <br>Center for Molecular Biophysics ORNL/UT <a href="http://cmb.ornl.gov">cmb.ornl.gov</a><br>
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