[gmx-users] Debugging 'inconsistent shifts'
kalev.takkis at gmail.com
Fri Jan 16 11:04:47 CET 2015
On 15 January 2015 at 19:44, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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.
>>>> 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
>>> 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
>> 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
> 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
It doesn't. Noticed the message in the terminal window when I was trying to
improve the visual with trjconv after the production run. Then went back
through the logs and found that it was first reported in NVE equilibration.
> 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 :)
No kidding. 1 step run -> 25MB log file. Fortunately grep was able to
extract the list of wonky atoms in a nice concise manner. Thank you for the
All the best,
> 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
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