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

[Justin Lemkul]

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 <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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>
>
>

-- 
==================================================

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

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