[gmx-developers] Hands-on Tutorial - Brazil - 04/11 - For David

David van der Spoel spoel at xray.bmc.uu.se
Sun Nov 9 14:07:37 CET 2008

Erik Marklund wrote:
> David van der Spoel skrev:
>> Elton Carvalho wrote:
>>> Hey there!
>>> David, what's the probability that gcc4.1 causes Gromacs (or some
>>> analysis tools) do 2+2=5 or something like that?
>>> Would this be the reason for the non-reproduction of the results at
>>> the tutorial sessions in São Carlos earlier this week, since those
>>> machines had gcc4.1 running?
>> Good point. I will try it on other machines first, but usually gcc 4 
>> causes SEGVs. If it is broken on other machines as well we have a 
>> problem, but probably localized in g_hbond.
> Hi,
> Intresting. There WAS a memory issue in g_hbond that involved writing 
> out of array bounds that cause SEGVs and outright erroneous results. The 
> fix did go into the development branch before the release of 4.0 and 
> also into the 3.3-patches as far as I know. Which version generated 
> irreproducible results at the tutorial?
The current release branch (4.0.1 soon te be 4.0.2) can not reproduce 
the numbers from my 2006 paper on alcohols. It seems the error is in the 
ACF rather than in the fitting procedure, as one can do the fitting 
manually with xmgrace which gives the same result as g_hbond. Hence the 
underlying data, the ACF must be wrong.

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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