On 3/12/18 1:40 PM, Viveca Lindahl wrote:
Hi Justin,

I'm using semi-isotropic pressure coupling and the periodicity is along z. I
should say that I'm also adaptively biasing a base pair to open, which is
triggering the fluctuations.

I guess you mean using only OpenMP? I have not tried that no, thanks for
the suggestion. Now I changed to Berendsen coupling which avoids the
problem (at least the fatal errors).

Yes, the problem is coming from either DD bookkeeping or actual instability. Trying with only OpenMP parallelization and therefore no domains will sort out whether it's physical or just a software problem. There's a lot going on if you've got periodic molecules, NPT, and a biasing potential, all with DD. Probably something no one has ever tested in GROMACS.

-Justin

--
Viveca


On Mon, Mar 12, 2018 at 3:46 PM, Justin Lemkul <jalem...@vt.edu> wrote:


On 3/12/18 10:42 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.

Periodic molecules are usually used in CNT systems or similar, and the
typical advice is to not apply pressure coupling along the long axis. I
suspect interactions get lost when the box fluctuates and the domain
topology does not get updated correctly. Does it work correctly with OpenMP?

-Justin


--
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
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Ph (404) 413-5491 | gp...@gsu.edu <mailto:gp...@gsu.edu>

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

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Virginia Tech Department of Biochemistry

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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

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