[gmx-users] mdrun : error

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> Hello,
> I am trying to do equilibration for my system (solvent + solute). I am
> geting the following error. If I run solvent and solute molecules
> separately, its run well. For mixture I am getting following error.
> What this error means.
> 
> Fatal error:
> 1 of the 22334 bonded interactions could not be calculated because some
> atoms involved moved further apart than the multi-body cut-off distance
> (0.8 nm) or the two-body cut-off distance (1 nm), see option -rdd, for
> pairs and tabulated bonds also see option -ddcheck
> 

Search the list archive.  This has been asked and answered several times, so 
you'll likely find something useful.  Also, take mdrun's advice and read about 
the options it's telling you.

-Justin

> NIlesh
> 

-- 
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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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