[gmx-developers] next Gromacs release
Erik Marklund
erikm at xray.bmc.uu.se
Tue Jun 15 14:15:38 CEST 2010
Rossen Apostolov skrev:
> Hi Erik,
>
> On 06/10/2010 10:12 PM, Erik Marklund wrote:
>> Hi,
>>
>> Hm. Embarassingly, it turns out that my posre-tpr didn't have any
>> position restraints. That sure explains it. I guess the bug can be
>> closed.
>>
>>
>> As for the g_hbond specifics, I first got error messages, then a
>> segfault. It's easily circumvented by adding the following check:
>> if (func_type == F_POSRES)
>> {
>> continue;
>> }
>> which i did put in my version, but it seems I forgot to push it. The
>> line that causes the problems reads:
>>
>> i+=interaction_function[top->idef.functype[interaction->iatoms[i]]].nratoms+1)
>> {
>> If interaction->iatoms[i] doesn't index idef.functype, then a lot of
>> things can happen.
>>
>> I'll push my gmx_hbond.c right away.
>>
> Did you already updated the file? Can you close the bug if so.
>
> Rossen
Done.
>> Erik
>>
>> Berk Hess skrev:
>>> 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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>>>>>> gmx-developers at gromacs.org
>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
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>>>>>> www interface or send it to gmx-developers-request at gromacs.org.
>>>>>>
>>>
>>
>>
>
--
-----------------------------------------------
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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