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

David van der Spoel spoel at xray.bmc.uu.se
Fri Mar 16 20:54:08 CET 2007

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 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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