[gmx-users] error message in mdrun: Check for bad contacts and/or reduce the timestep if appropriate.

Justin Lemkul jalemkul at vt.edu
Sun May 4 18:09:28 CEST 2014

On 5/4/14, 11:42 AM, Nizar Masbukhin wrote:
> Hi friends,
> I am calculating free energy of a protein. I got this message when i run mdrun. My command was  mdrun -deffnm npt -nt 1
> Step 2, time 0.004 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000022, max 0.000500 (between atoms 2240 and 2243)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>     2844   2845   39.8    0.1105   0.1090      0.1090
> step 2: Water molecule starting at atom 41058 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> I have reduced nsteps from 5000 to 10000, but the same error message appeared

As you should expect - if your failure is at step 2, then changing the number of 
steps from 10000 to 5000 should not change anything!

What do you mean "calculating the free energy of a protein?"  Are you trying to 
decouple an entire protein?  That would be extremely difficult and unlikely to 
succeed.  What is in your .mdp file?



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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