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 | gp...@gsu.edu <mailto:gp...@gsu.edu>
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