[gmx-users] Domain decomposition error

[Dawid das]

Well, I do not do anything special when preparing this system compared to
other systems that do not show this issue.

I have carefuly inspected my system and I know what is wrong. I did some
manipulations to PDB file due to missing fragment of
residue and accidentally put NZ atom of Lysine like 3.5 nm from the
side-chain carbon...

Sorry for bothering.

Best wishes,
Dawid

2018-04-15 16:41 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 4/15/18 9:29 AM, Dawid das wrote:
>
>> Dear Gromacs Users,
>>
>> I run numerous MD simulations for similar systems of protein in water box
>> and
>> for only one system I encounter error:
>>
>>
>>
>>
>>
>> *Fatal error:There is no domain decomposition for 4 ranks that is
>> compatible with the givenbox and a minimum cell size of 3.54253 nmChange
>> the number of ranks or mdrun option -rddLook in the log file for details
>> on
>> the domain decomposition*
>>
>> I found explanation of this error in Gromacs documentation as well as on
>> the mailing
>> list, however I still do not understand why I get this only for one system
>> out of many.
>> There is nothing special about it, I mean its size for instance is similar
>> to this of
>> others systems.
>>
>> What can be source of this error, then? Can it be the system size or
>> placement of
>> charge groups?
>>
>
> A "normal" protein-in-water system will never have such a minimum cell
> size unless you're doing something unconventional, like long-distance
> restraints, free energy calculation adding explicit intramolecular
> exclusions, or some weird topology element that is not conventional. If you
> can give more details (and the information from the .log file about how DD
> is determining this minimum cell size), we can probably say more.
>
> -Justin
>
> --
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
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