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

[Nizar Masbukhin]

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
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My Best Regards, Nizar
Medical Faculty of Brawijaya University, Malang, Indonesia