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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