[gmx-developers] next Gromacs release

[Berk Hess]

Hi,

For a tpr I made it works fine.
Could you attach a tpr to the bugzilla?

I already noticed the lacking documentation in idef.h, I fixed that now.

Berk

Erik Marklund wrote:
> Hi,
>
> I suspected something along those lines. But why then is
> top->idef.iparams_posres == NULL? g_hbond reads the tpr-file with
> read_tpx_top, which in turn calls read_tpx() and
> gmx_mtop_t_to_t_topology(). Here's what I spot when running gdb:
>
> 1057                interaction=&(top->idef.il[func_type]);
> (gdb) p top->idef    $1 = {
>  ntypes = 412,
>  atnr = 16,
>  functype = 0x1002000,
>  iparams = 0x799000,
>  fudgeQQ = 0.833299994,
>  cmap_grid = {
>    ngrid = 0,
>    grid_spacing = 0,
>    cmapdata = 0x0
>  },
>  iparams_posres = 0x0,       <==== Lookie here!
>  iparams_posres_nalloc = 0,
> ...
>
> This suggests that the posres stuff isn't passed to the t_topology
> properly. Dunno if this is a big issue for the analysis tools though.
>
> Furthermore, if this is not a bug then I think one should extend the
> unusually descriptive comment in idef.h to make it clear that the
> t_ilist indexes the ipatams_posres[], and not params and functype[] as
> the comment now states:
>
> /*
> * The struct t_ilist defines a list of atoms with their interactions.
> * General field description:
> *   int nr
> *      the size (nr elements) of the interactions array (iatoms[]).
> *   t_iatom *iatoms
> *      specifies which atoms are involved in an interaction of a certain
> *       type. The layout of this array is as follows:
> *
> *       
> +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
> *       
> |type1|at1|at2|at3|type2|at1|at2|type1|at1|at2|at3|type3|at1|at2|
> *       
> +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
> *
> *      So for interaction type type1 3 atoms are needed, and for type2
> and
> *      type3 only 2. The type identifier is used to select the
> function to
> *      calculate the interaction and its actual parameters. This type
> *      identifier is an index in a params[] and functype[] array.
> */
>
> hess at sbc.su.se skrev:
>> Hi,
>>
>> Due to the molecular topology change for 4.0
>> posres now indexing into idef.iparams_posres iso idef.iparams.
>> This is required, because position restraints are the only
>> interactions with different parameters for each molecule.
>>
>> Berk
>>
>>  
>>> I found a new bug while attempting to fix bug 334 and submitted a new
>>> bugzilla (http://bugzilla.gromacs.org/show_bug.cgi?id=428). I'm not
>>> entirely sure this is a bug, or the way it's intended, but the t_ilist
>>> contains strange things when the a tpr file is generated with position
>>> restraints. I can easily make a fix for this in gmx_hbond.c, but that's
>>> not how to mend broken things if the error really is in grompp.
>>>
>>> To summarize, top->idef.il[F_POSRES] dereferences the wrong functypes.
>>> For my test system it dereferences LJ (SR):
>>>
>>>   (gdb) p top->idef.il[44].iatoms[0]
>>>   $31 = 0
>>> ...
>>>   (gdb) p top->idef.functype[0]
>>>   $36 = 31
>>>   (gdb) p interaction_function[31].longname
>>>   $37 = 0x5fa3ba "LJ (SR)"
>>>
>>> Is this really the way it should be?
>>>
>>> Erik
>>>
>>> Rossen Apostolov skrev:
>>>    
>>>> To all developers,
>>>>
>>>> The new release of Gromacs is coming close. Before releasing the new
>>>> packages though, in the next couple of weeks until June 15:
>>>>
>>>> * everything in bugzilla should be cleared (David already started
>>>> exterminating :). If you see a bug that you can fix or help with,
>>>> please do so.
>>>> * if there are still any known issues, please file a bug asap or send
>>>> a patch.
>>>> * do not add any new features! Berk has some AmberFF stuff but apart
>>>> from that everything new should wait for the next release
>>>> * make sure that everything compiles without warnings on all platforms
>>>> that you have access to
>>>>
>>>> Hopefully all that will be done by the 15th and have a bug-free
>>>> summer:)
>>>>
>>>> Cheers,
>>>> Rossen
>>>>       
>>> -- 
>>> -----------------------------------------------
>>> Erik Marklund, PhD student
>>> 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://folding.bmc.uu.se/
>>>
>>> -- 
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>>>
>>>     
>>
>>   
>
>