[gmx-users] Debugging 'inconsistent shifts'

[Justin Lemkul]

On 1/15/15 11:25 AM, Kalev Takkis wrote:
> On 15 January 2015 at 00:09, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 1/14/15 4:44 PM, Kalev Takkis wrote:
>>
>>> Hi, list!
>>>
>>> GROMACS complains about inconsistent shifts and suggests me to check my
>>> topology. I have so done, but the problem is not immediately obvious. How
>>> can I make it tell me exactly which atoms/bonds it finds faulty?
>>>
>>>
>> What were you doing when the error came up?  What was your exact command?
>> What is your system?
>>
>
> Temperature equilibration, commands given were
>       gmx grompp -f nvt.mdp -c simcell_minim.gro -p simcell.top -o
> simcell_temp.tpr
>       gmx mdrun -v -deffnm simcell_temp
>
> GROMACS version 5.0.4, ff OPLS-AA
> Equilibration finishes without other problems, I can continue with the next
> step without the system blowing up. The error is not encountered during
> minimisation, it finishes fine, energies are reasonable and no trace of
> inconsistent shifts is found in the log.
> System is chromatography column, silica slab with attached hydrocarbon
> chains. The crystal surface is infinite in xz plane, so the mdp file
> specifies
> pbc             = xyz
> periodic_molecules = yes
>

Have you verified that all the bonded terms that span a periodic boundary are 
specified correctly?

> The model is hacked together from silica unit cell and chains using
> pdb2gmx, so it's entirely possible that there is indeed something wrong
> with my system. I'd like to know where. When GROMACS encounters this error

The topology is the first and most likely source of error.

> can I make it reveal more details? Which atoms/bonds are involved? Some
> diagnostics tool or verbosity switch to mdrun maybe?
>

How soon does the system blow up?  General troubleshooting advice is at 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

All GROMACS tools have a -debug flag that can be set, but you'll dump out a 
massive file with a ton of information you don't need.  If you're not used to 
reading through it, it can be more of an obstacle than a useful tool :)

-Justin

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

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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