[gmx-users] genconf and bonded interactions

Justin A. Lemkul jalemkul at vt.edu
Wed Jul 27 14:45:56 CEST 2011


The problem is indeed as I suspected.  Your molecules are broken across periodic 
boundaries in the initial configuration.  When you replicate with genbox, you've 
now replicated broken molecules such that those at the new interfaces between 
the boxes appear to be intact, but in fact they are not.  This is just an 
artifact of visualization.  If you use "trjconv -pbc whole" on the original 
starting configuration to make the molecules whole before replicating with 
genconf -nbox, you will avoid this problem.

-Justin

Fabio Affinito wrote:
> Yes. It's in attachment.
> 
> Fabio
> 
> On 07/27/2011 02:38 PM, Justin A. Lemkul wrote:
>>
>> Can you please also send me the coordinate file from before you ran
>> genconf?
>>
>> -Justin
>>
>> Fabio Affinito wrote:
>>> Finally, I just got the right compression to fit my file in an
>>> attachment.
>>> The interesting lines are:
>>> 159988 and 159992
>>>
>>> Kindly regards,
>>>
>>> Fabio
>>>
>>> On 07/27/2011 01:42 PM, Justin A. Lemkul wrote:
>>>>
>>>>
>>>> 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
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>
> 
> 

-- 
========================================

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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