[gmx-users] genconf and bonded interactions

[Fabio Affinito]

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.

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
>>>>>
>>>>
>>>>
>>>
>>
>>
>


-- 
Fabio Affinito, PhD
SuperComputing Applications and Innovation Department
CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY
Tel: +39 051 6171794  Fax: +39 051 6132198