[gmx-users] A charge group moved too far between two domain decomposition steps

[Justin Lemkul]

On 11/6/12 10:42 PM, Ali Alizadeh wrote:
> Dear All users
>
> I used OPLS ff for my system and I did not break my bonds,
>
> When i use gromos96 45a3 after minimizing my bonds break(i can see
> em.gro) but i do not get any errors in this step
>

Bonds do not break during MD.  Probably what you're seeing is a periodicity effect.

> After md production i get this error:
>
> Fatal error:
> A charge group moved too far between two domain decomposition steps
> This usually means that your system is not well equilibrated
>
>

Lots of information on the Gromacs website:

http://www.gromacs.org/Documentation/Errors#A_charge_group_moved_too_far_between_two_domain_decomposition_steps.

...and also in the list archive.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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