[gmx-users] Help with interpreting message for fatal error

[Gregory Poon]

Since there hasn't been any response to your question yet, may I ask: is 
it reproducible?

Gregory


On 3/11/2018 7:30 AM, Viveca Lindahl wrote:
> Hi,
>
> I'm running a simulation of a periodic DNA molecule. After some time I get,
> sometimes the following error message:
>
> ---------------
>
> A list of missing interactions:
>           Proper Dih. of   3917 missing      1
>
> Molecule type 'DNA_chain_A'
> the first 10 missing interactions, except for exclusions:
>           Proper Dih. atoms  414  417  418  421 global   414   417   418
> 421
>
> -------------------------------------------------------
> Program:     gmx mdrun, version 2018.1-dev-20180306-33093601f
> Source file: src/gromacs/domdec/domdec_topology.cpp (line 436)
> MPI rank:    0 (out of 32)
>
> Fatal error:
> 1 of the 10381 bonded interactions could not be calculated because some
> atoms
> involved moved further apart than the multi-body cut-off distance (0.5465
> nm)
> or the two-body cut-off distance (1.093 nm), see option -rdd, for pairs and
> tabulated bonds also see option -ddcheck
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FDocumentation%2FErrors&data=02%7C01%7Cgpoon%40gsu.edu%7C18eac9ccdd4b479d86c708d5875cbb61%7C515ad73d8d5e4169895c9789dc742a70%7C0%7C0%7C636563754716997653&sdata=wUdEASAxNIPHNAmQwBO8EO0Ec8EI%2FVdjY7f7i9R0IYc%3D&reserved=0
> -------------------------------------------------------
> Rank 0 [Sun Mar 11 13:37:32 2018] [c0-0c1s3n0] application called
> MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> _pmiu_daemon(SIGCHLD): [NID 00076] [c0-0c1s3n0] [Sun Mar 11 13:37:32 2018]
> PE RANK 0 exit signal Aborted
> [NID 00076] 2018-03-11 13:37:32 Apid 12709959: initiated application
> termination
> Application 12709959 exit codes: 134
> Application 12709959 resources: utime ~1083s, stime ~16s, Rss ~21376,
> inblocks ~34261, outblocks ~55016
> ---> Reached end of run script.
>
>
> How should I... proceed here? Is my system set up poorly, is it a bug in
> mdrun? Suggestions appreciated.
>
> --
> Viveca
-- 

*Gregory M. K. Poon, PhD, RPh*
Associate Professor
Departments of Chemistry and Nutrition | Georgia State University
NSC 414/415/416 | 50 Decatur St. SE, Atlanta, GA 30302
P.O. Box 3965 | Atlanta, GA 30303
Ph (404) 413-5491 | gpoon at gsu.edu <mailto:gpoon at gsu.edu>