[gmx-users] genconf and bonded interactions

[Justin A. Lemkul]

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.

> 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?

-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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