[gmx-users] Re: system blowing up

Shima Arasteh shima_arasteh2001 at yahoo.com
Sat Jul 28 17:18:15 CEST 2012

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

Thanks for your suggestions.


----- Original Message -----
From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
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.

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