[gmx-users] genconf and bonded interactions

[Fabio Affinito]

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?

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