It's a little bit challenging trouble I've got into! Of course for me.

Thanks for your suggestions.

 
Sincerely,
Shima


----- Original Message -----
From: Mark Abraham <mark.abra...@anu.edu.au>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Cc: 
Sent: Saturday, July 28, 2012 7:23 PM
Subject: Re: [gmx-users] Re: system blowing up

On 29/07/2012 12:51 AM, Dr. Vitaly V. G. Chaban wrote:
>> Thanks for your reply.
>>
>> I'm following the protocol of Diagnosing an unstable system. Corresponding 
>> the first step I changed th nstxout to 1 for 3 times.
>> The first and second time I got error the same as before ( some interactions 
>> seem to be assigned multiple times ) and it the warning as below was 
>> appeared:
>>
>> Warning: 1-4 interaction between 5 and 18 at distance 2.017 which is larger 
>> than the 1-4 table size 2.000 nm
>>
>> For the third time, I did'nt get any error and the output files were 
>> generated without any warning or error.
>>
>>
>> Is it acceptable to go on with these outputs? Why such a thing happened? Is 
>> the system minimized sufficiently after 2 times?
>>
>
> decrease your time-step

That's not likely to help if there's an initial bond of length 0.35nm.

Mark
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