[gmx-users] xx of the xxxx bonded interactions couldn't be calculated

[Justin Lemkul]

On 6/6/13 10:00 PM, Badamkhatan wrote:
> Dear GMX-users
>
> Recently i got this error and note from my MD2 simulation. I'm solvating
> 1-octanol to 1-octanol and calculating free energy differences. This is the
> last step of my calculation and previous steps are looking fine. Basically i
> followed Justin's free energy tutorial.
> Here is
> Note:
>   A list of missing interactions:
>          LJC Pairs NB of    210 missing      1
>            exclusions of  25308 missing      1
>
> Molecule type '1-octanol'
> the first 10 missing interactions, except for exclusions:
>          LJC Pairs NB atoms    3   25           global     3    25
>
> Fatal error:
> 2 of the 57736 bonded interactions could not be calculated because some
> atoms involved moved further apart than the multi-body cut-off distance (1
> nm) or the two-body cut-off distance (1 nm), see option -rdd, for pairs and
> tabulated bonds also see option -ddcheck
>
> Please help me and suggest any idea to solve this problem?
>

Sounds like you're http://www.gromacs.org/Documentation/Terminology/Blowing_Up.

-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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