[gmx-users] Fatal error: * of the *** bonded interactions could not be calculated because ...

[Chang Woon Jang]

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
options, the simulation goes well but the simulation trajectory seem weird
that some molecules are going out the simulation box

    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 <jalemkul at 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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
Best regards,
Changwoon Jang,

Postdoctoral Research Fellow
Department of Chemical & Biological Engineering, Drexel University
3141 Chestnut Street, Philadelphia, PA 19104

Voice: (662) 617-2267
E-mail: cj395 at drexel.edu