[gmx-users] genconf and bonded interactions

[Justin A. Lemkul]

Fabio Affinito wrote:
> On 07/26/2011 07:02 PM, Justin A. Lemkul wrote:
>>
>>
>> Fabio Affinito wrote:
>>> On 07/26/2011 05:06 PM, Justin A. Lemkul wrote:
>>>>
>>>>
>>>> Fabio Affinito wrote:
>>>>> Maybe this is a different issue... but it's ok that after the 99,999th
>>>>> atom the counter restarts from zero?
>>>>>
>>>>>> 21374SOL OW99999 12.986 9.021 7.036 -0.0037 -0.4345 0.3977
>>>>>> 21374SOL HW1 0 13.069 8.987 7.081 0.5916 0.5409 0.0638
>>>>>
>>>>> Could this be the origin of my problem?
>>>>>
>>>>
>>>> Atom numbering is not the problem. This happens all the time for 
>>>> systems
>>>> of hundreds of thousands of atoms, which Gromacs handles just fine.
>>>> Please investigate the points I suggested before.
>>>
>>> Yes, but this doesn't make things easier! :-)
>>> According to the log the atoms to consider are 159986 and 159990
>>>
>>
>> That's not what you posted before. The .log output indicated atoms
>> 193657 and 193660 were problematic.
> 
> Sorry. It's because I've tried with many systems (with different -nbox 
> values) and the error was always the same.
> 
>>
>>> Browsing the conf.gro, if I didn't make mistakes this atoms are:
>>>
>>>> 30040POPG OE59986 0.080 13.158 2.964 0.0885 0.4154 -0.0859
>>>
>>>> 30040POPG C1C59990 0.219 26.034 3.221 0.6449 0.0750 0.1313
>>>
>>> But their distance is 12.8nm, while md.log reports 38.911 nm...
>>>
>>
>> In any case, why are atoms four bonds (based on the original .log output
>> of 1-4 interactions being a problem) away separated by 12.8 nm? Seems
>> very odd to me. I ask yet again - what are your box vectors, before and
>> after manipulation with genconf?
> 
> 
> Seems odd to me, too. For the box vectors (sorry if I didnt answer 
> before), in  this case:
> 
> after:   26.04658  26.04658   8.75317
> before:  13.02329  13.02329   8.75317
> 
> Hope it helps.
> 

Without seeing the coordinate files, I can't tell anything further.  If you 
want, you can send me (off-list) the coordinate files before and after genconf 
and please tell me the exact atoms that are reported as problematic.

-Justin

> Best regards,
> 
> Fabio
> 
>>
>> -Justin
>>
>>> So what?
>>>
>>> F.
>>>
>>>
>>>
>>>
>>>>
>>>> -Justin
>>>>
>>>>> Thanks again,
>>>>>
>>>>> Fabio
>>>>>
>>>>> On 07/26/2011 04:38 PM, Justin A. Lemkul wrote:
>>>>>>
>>>>>>
>>>>>> Fabio Affinito wrote:
>>>>>>> On 07/26/2011 04:30 PM, Justin A. Lemkul wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>> Fabio Affinito wrote:
>>>>>>>>> On 07/26/2011 04:19 PM, Justin A. Lemkul wrote:
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Were the molecules whole in the coordinate file you 
>>>>>>>>>> replicated? If
>>>>>>>>>> not,
>>>>>>>>>> the bonds will now be assigned across the entire box.
>>>>>>>>>>
>>>>>>>>>> -Justin
>>>>>>>>>>
>>>>>>>>> Yes and not, depending on what you mean by "whole".
>>>>>>>>> It is an ion channel, so it's made of four chains.
>>>>>>>>> This clarifies? (i guess not..)
>>>>>>>>
>>>>>>>> By whole, I mean that the molecules are not split across periodic
>>>>>>>> boundaries in the initial configuration that you replicated. If you
>>>>>>>> replicate a periodic break, then you split the molecules by a
>>>>>>>> distance
>>>>>>>> equal to the new periodic distance.
>>>>>>>>
>>>>>>>> -Justin
>>>>>>>>
>>>>>>> Ok, so: no, it's not broken.
>>>>>>>
>>>>>>
>>>>>> What you need to do is use the information mdrun provided you to
>>>>>> diagnose what's going on. Apparently atoms 193657 193660 are 
>>>>>> separated
>>>>>> by 31 nm. What are your box vectors? Where are these atoms in the
>>>>>> system? Then you'll have your answer. The only reason I can think
>>>>>> of for
>>>>>> such extreme distances is a periodicity issue.
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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