On 8/30/16 11:52 AM, Chang Woon Jang wrote:
Dear Justin Lemkul,
Thank you for your answers. The following is the error message after I
run " gmx mdrun -s topol.tpr -c confgout.gro -o traj.trr -x traj.xtc -rdd
2.5".
Initializing Domain Decomposition on 8 ranks
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Minimum cell size due to bonded interactions: 2.500 nm
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 8 cells with a minimum initial size of 3.125 nm
The maximum allowed number of cells is: X 1 Y 1 Z 1
-------------------------------------------------------
Program gmx, VERSION 5.0.8-dev-20151014-1f04b58
Source code file:
/home/chang/PACKAGE/votca/src/gromacs/src/gromacs/mdlib/domdec.c, line: 6902
Fatal error:
There is no domain decomposition for 8 ranks that is compatible with the
given box and a minimum cell size of 3.125 nm
Change the number of ranks or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
And what does Google tell you about this particular case? Hint: the same error
gets posted to this list pretty much weekly, if not more often. It's been
rationalized and solved time and time again.
-Justin
Best regards,
Changwoon Jang
On Tue, Aug 30, 2016 at 11:30 AM, Justin Lemkul <jalem...@vt.edu> wrote:
On 8/30/16 10:41 AM, Chang Woon Jang wrote:
Dear Justin Lemkul,
Thank you for your response. Yes, I use coarse-grained system
(thermosetting polymer). I prepared the system from the equilibrated
atomistic system. The atomistic system was equilibrated using OPLS-AA
force
filed under NPT and NVT for almost 40 ns. The initial atomistic system
contained 13854 atoms. The equilibrated atomistic system was
coarese-grained (mapped) with certain criteria. Now, I am trying to get CG
potentials using iterative Boltzmann Inversion, but this error keeps me
dizzy.
Whenever I use -rdd options, it gives another error like domain
decomposition error with other options recommended. Whenever I use -nt
Please always post exact error messages, copied and pasted directly from
the terminal or .log file. We can't guess at what you're reading.
options, the simulation goes well but the simulation trajectory seem weird
that some molecules are going out the simulation box
This is just PBC. There is no "outside" of a box. If you've got
polymers, they will elongate and contract depending on their physical
behavior. There's nothing wrong with that.
-Justin
It seems tricky to find what is the problem.
Thank you.
Best regards,
Changwoon Jang
On Tue, Aug 30, 2016 at 8:37 AM, Justin Lemkul <jalem...@vt.edu> wrote:
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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send a mail to gmx-users-requ...@gromacs.org.
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==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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