[gmx-users] genconf and bonded interactions

[Fabio Affinito]

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

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...

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