[gmx-users] Debugging 'inconsistent shifts'

Kalev Takkis kalev.takkis at gmail.com
Thu Jan 15 17:25:19 CET 2015

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
     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
pbc             = xyz
periodic_molecules = yes

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

All the best,

> -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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