Hi Viveca,

Could you share more details of your simulations that may shed any light?  I assume that you are using parmbsc1 as the DNA forcefield.  Is it an "unusual" system?  We (and I am sure others) simulate DNA (± ligand) quite a bit and would be as interested in understanding what is going wrong here, although I have never encountered what you are observing.

Best wishes,

Gregory


On 3/12/2018 7:42 AM, Viveca Lindahl wrote:
Hi Gregory,

In the sense that I see it happening repeatedly yes :) But I can't
reproduce it very predictably.

After seeing that (for my small system) I get very large box vector
fluctuations using Parrinello-Rahman, my current assumption is that there
are some stability assumptions made by mdrun internally that are being
violated.
I would still be interested in understanding what actually goes wrong
though.

--
Viveca


On Mon, Mar 12, 2018 at 4:49 PM, Gregory Poon <gp...@gsu.edu> wrote:

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%7C515ad
73d8d5e4169895c9789dc742a70%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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--

*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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