[gmx-users] Energy minimization error

[Kavyashree M]

Ok thanks

On Fri, Apr 15, 2011 at 9:56 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Kavyashree M wrote:
>
>> Dear gromacs users,
>>
>> While doing energy minimization for a protein (from pdb), with oplsaa
>> force field
>> and tip4p water model, there was an error and em stopped -
>>
>> Fatal error:
>> A charge group moved too far between two domain decomposition steps
>> This usually means that your system is not well equilibrated
>>
>> What is the correction for this?
>>
>>
> Build a more reasonable starting structure.  Somewhere you have atomic
> overlap or otherwise unresolvable geometry such that you have atoms flying
> across the system, as the error message indicates (although somewhat
> obliquely).
>
> The screen/log output from mdrun should print where the high forces are, or
> which atoms are having constraint problems, etc.  Investigate these atoms in
> your starting structure and/or EM trajectory and determine an appropriate
> solution based on what you find.
>
> -Justin
>
>
>  Thanking you
>> With regards
>> kavya
>>
>>
> --
> ========================================
>
> 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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