[gmx-users] problem regarding "mdrun" and "g_hbond"

Tsjerk Wassenaar tsjerkw at gmail.com
Sat Mar 17 20:13:29 CET 2007

Hi David,

Of course, it's not a dogma... But in your case, it will be well
thought over. That makes the difference. (From another point of view,
if the simulation system is small, often you'll still want temperature
coupling anyway...). Anyway, as with all gromacs warnings, they should
just make you think about the things you're doing. If you know it's
what you want, you can always ignore'm.


On 3/16/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> Mark Abraham wrote:
> >> I think a warning is a good idea, but maybe 10 is even on the low side
> >> for that. Since temperature is macroscopic, you'll need enough atoms
> >> not to deviate too much from the target temperature. I have no
> >> evidence on which I can make a proper suggestion... My bidding will be
> >> 50! Going once, going twice... (maybe someone has looked more into
> >> this matter. David, Berk?).
> >
> > I added a bugzilla enhancement-request for this feature, suggesting that
> > if the user tries 3+ T-coupling groups where the smallest is less than 10%
> > of the smaller of the other two then we probably have a case of bad
> > planning from the user, and should give a warning. Doubtless there are
> > better ideas out there... it's after midnight here!
> I've implemented the 10% of atoms test. Could be changed to a fixed
> number of atoms as well. Not sure which one makes more sense (I quite
> often simulate systems that fall under the fixed atom limit (didn't
> Tsjerk say 50?)).
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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