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

[Erik Marklund]

David van der Spoel skrev:
> 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.
>
What about the hbond existence matrix? One could use that raw data with 
a bit of coding/scripting to produce one's own ACF, just to double 
check. There has been a fix for a bug where the last occurence of each 
hbond was lost. When hbonds are rare that error could be significant (i 
think).

What about 4.0.0? Can it reproduce the numbers?

-- 
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys