[gmx-users] Fatal error: * of the *** bonded interactions could not be calculated because ...

[Justin Lemkul]

On 8/29/16 6:02 PM, Chang Woon Jang wrote:
> Dear Gromacs Users,
>
>
> I have a Fatal error as follow. The error says -rdd option or -ddcheck. How
> can I properly use these options? Is the following command the proper use
> of these options?
>
>> gmx mdrun -s topol.tpr -c confout.gro -o traj.trr -x traj.xtc -rdd 1.5
> -ddcheck
>

Yes, but note that -ddcheck is on by default anyway, and you should look into 
why this might be happening.  You can get around this error, but it often 
indicates instability.  Without a complete description of what your system is, 
what you've previously done to prepare, minimize, equilibrate, etc. we're sort 
of just guessing here.  If the system is coarse grain, then use of a large -rdd 
is typical (as you will see from many threads in the archive that address this 
case specifically).

-Justin

> Thank you.
>
>
> 1 of the 1612 bonded interactions could not be calculated because some
> atoms involved moved further apart than the multi-body cut-off distance
> (1.5 nm) or the two-body cut-off distance (1.5 nm), see option -rdd, for
> pairs and tabulated bonds also see option -ddcheck
> For more information and tips for troubleshooting, please check the GROMACS
>
>
>
>
> Best regards,
> Changwoon Jang,
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================