[gmx-users] genconf and bonded interactions

[Justin A. Lemkul]

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.

-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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