[gmx-developers] next Gromacs release

[Erik Marklund]

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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>>
>>     
>
>   


-- 
-----------------------------------------------
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/