[gmx-users] mdrun : error

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 12 02:48:52 CEST 2010

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.


> NIlesh


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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