[gmx-users] Re: Inconsisten shift Error

[Justin A. Lemkul]

teklebrh at ualberta.ca wrote:
> 
> Hi Justin,
> 
> My system is -- simulation a polymer (called PAP) in toluene (TOL)... to 
> see the aggregation behavior of the molecule in TOL.
> 
> the PAP molecule contains 55 atoms.......
> 
> I inserted 8 PAP molecule in a Toluene ..... it works fine.
> 
> Energy minimization .... it works fine (to the entire system)
> 

Define "fine" - what were the values of the potential energy and maximum force?

> I am using the ffgmx force field.....
> 

Why?  This force field has long been deprecated.

> I used a 10 X 10 X 10 both with a total of 29749 atoms in the box......
> 
> when I start equilibrating my system using NVT ... I got that error.....
> 
> Initially I used the berendsen thermostat and got an error of 
> segmentation fault but I changed the thermostat as recommended in the 
> error to V-rescaling and got this error.......
> 

For initial equilibration, either should be fine, but the fact that the system 
crashes suggests that there is something physically unrealistic about the 
system.  Change nstxout to 1 and try to capture some frames of what's going 
wrong, to see where the crash starts.  Otherwise, consider how you developed the 
parameters for both PAP and TOL - did you validate them?  Are they appropriate?

-Justin

> That is it......
> 
> Regards,
> 
> Rob
> 
> 
> 
> 
> 
> 
> 
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
> 
>>
>>
>> teklebrh at ualberta.ca wrote:
>>> Hi Justin,
>>>
>>> I just checked this error on the archive list but could not found a 
>>> reasonable answer ......
>>>
>>> I have done the energy minimization and it is ok Fmax less than 100
>>>
>>> but when I start equilibrating my system I got the following error..
>>>
>>> =================================================
>>> There were 2 inconsistent shifts. Check your topology
>>>
>>> Warning: 1-4 interaction between 18851 and 18856 at distance 42.558 
>>> which is larger than the 1-4 table size 1.900 nm
>>>
>>> These are ignored for the rest of the simulation
>>>
>>> This usually means your system is exploding,
>>>
>>
>> Here's the usual advice:
>>
>> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
>>
>> <snip>
>>
>>> tcoupl                   = V-rescale ; modified berendsen thermostat
>>> ; Groups to couple separately
>>> tc-grps                  = PAP TOL
>>
>> What are PAP and TOL?  Are they of sufficient size to justify their 
>> own temperature coupling groups?
>>
>> http://www.gromacs.org/Documentation/Terminology/Thermostats
>>
>> Other than that, you'll have to give some information about what your 
>> system is, how you built it, and what parameters (force field) you're 
>> using.
>>
>> -Justin
>>
>> -- 
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> 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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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