[gmx-users] fatal error: 1 particles communicated to PME node 1 are more than a cell length out of the do main decomposition cell of their charge group

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> Actullay I started with 1.0-nm cutoff for  Coulomb and vdW. Its giving
> error for cutoff value and box size (increase the box size or reduce the
> cutoff). I can't change the box size because density of system also
> changes so I reduced the cutoff value.
> 
> 

You can't haphazardly change the cutoff values.  They are prescribed by the 
force field you're using.  You shouldn't have a density issue if you equilibrate 
sufficiently.  Bottom line: use a bigger box and appropriate cutoffs, or else 
your results are questionable, at best.

-Justin

> 
> On Fri, September 4, 2009 4:49 pm, Justin A. Lemkul wrote:
> 
>> Nilesh Dhumal wrote:
>>
>>> Hello,
>>>
>>>
>>> I am trying to equilibrate a ionic liquid system (EMI-BF4) in Gromacs
>>> 4.0.5 version.  The  minimization went OK, but in the equilibration at
>>> constant pressure
>>>
>> <snip>
>>
>>
>>> rlist               =  0.6 coulombtype         = PME vdwtype
>>> = cut-off
>>> rcoulomb            =  0.6 rvdw                =  0.6
>> What motivated these cutoff values?  These are shorter than any I've ever
>> seen (some of the older AMBER publications used a 0.7-nm cutoff for
>> Coulomb and vdW);
>> could be causing problems, especially in the setup of domain
>> decomposition.
>>
>> -Justin
>>
>>
>> --
>> ========================================
>>
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
>> ========================================
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> 
> 
> 

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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