# Step 13 and step 28: One or more water molecules can not be settled

**URL:** <https://gromacs.bioexcel.eu/t/step-13-and-step-28-one-or-more-water-molecules-can-not-be-settled/9033>\
**Category:** User discussions\
**Tags:** mdrun, energy-minization\
**Created:** [May 1, 2024, 9:31am UTC](https://gromacs.bioexcel.eu/t/step-13-and-step-28-one-or-more-water-molecules-can-not-be-settled/9033 "2024-05-01T09:31:56Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Krunal](https://avatars.discourse-cdn.com/v4/letter/k/ce7236/32.png) [@Krunal](https://gromacs.bioexcel.eu/u/Krunal)\
**Post date:** [May 1, 2024, 9:31am UTC](https://gromacs.bioexcel.eu/t/step-13-and-step-28-one-or-more-water-molecules-can-not-be-settled/9033/1 "2024-05-01T09:31:56Z")

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GROMACS version:  
GROMACS modification: Yes/No  
Please suggest do i need to take any action or i can ignore and go ahed with below step 13: One or more water molecules can not be settled. and step 28: One or more water molecules can not be settled?:  
Steepest Descents:  
Tolerance (Fmax) = 1.00000e+03  
Number of steps = 50000  
Step= 0, Dmax= 1.0e-02 nm, Epot= 6.60209e+07 Fmax= 1.60721e+10, atom= 17222  
Step= 1, Dmax= 1.0e-02 nm, Epot= -2.03359e+06 Fmax= 2.30368e+08, atom= 17222  
Step= 2, Dmax= 1.2e-02 nm, Epot= -3.35475e+06 Fmax= 5.27653e+06, atom= 17222  
Step= 3, Dmax= 1.4e-02 nm, Epot= -3.43058e+06 Fmax= 1.36737e+06, atom= 17207  
Step= 4, Dmax= 1.7e-02 nm, Epot= -3.54372e+06 Fmax= 3.52260e+05, atom= 17223  
Step= 5, Dmax= 2.1e-02 nm, Epot= -3.81030e+06 Fmax= 8.36361e+04, atom= 17261  
Step= 6, Dmax= 2.5e-02 nm, Epot= -4.19820e+06 Fmax= 2.30693e+04, atom= 9949  
Step= 7, Dmax= 3.0e-02 nm, Epot= -4.50048e+06 Fmax= 3.03997e+04, atom= 17255  
Step= 8, Dmax= 3.6e-02 nm, Epot= -4.58450e+06 Fmax= 3.24510e+04, atom= 17255  
Step= 9, Dmax= 4.3e-02 nm, Epot= -4.64982e+06 Fmax= 1.59175e+04, atom= 17255  
Step= 10, Dmax= 5.2e-02 nm, Epot= -4.76073e+06 Fmax= 5.54114e+04, atom= 17255  
Step= 11, Dmax= 6.2e-02 nm, Epot= -4.78947e+06 Fmax= 1.37796e+04, atom= 17255  
Step= 12, Dmax= 7.4e-02 nm, Epot= -4.88564e+06 Fmax= 1.00211e+05, atom= 9205

step 13: One or more water molecules can not be settled.  
Check for bad contacts and/or reduce the timestep if appropriate.  
Wrote pdb files with previous and current coordinates  
Step= 14, Dmax= 4.5e-02 nm, Epot= -4.90195e+06 Fmax= 3.53101e+04, atom= 92055  
Step= 15, Dmax= 5.3e-02 nm, Epot= -4.92461e+06 Fmax= 3.60905e+04, atom= 9205  
Step= 16, Dmax= 6.4e-02 nm, Epot= -4.94646e+06 Fmax= 4.94189e+04, atom= 9205  
Step= 17, Dmax= 7.7e-02 nm, Epot= -4.96493e+06 Fmax= 5.51652e+04, atom= 9205  
Step= 18, Dmax= 9.2e-02 nm, Epot= -4.98156e+06 Fmax= 6.76785e+04, atom= 9205  
Step= 19, Dmax= 1.1e-01 nm, Epot= -4.99492e+06 Fmax= 1.24357e+05, atom= 9205  
Step= 20, Dmax= 1.3e-01 nm, Epot= -5.01060e+06 Fmax= 8.10146e+04, atom= 9205  
Step= 21, Dmax= 1.6e-01 nm, Epot= -5.02085e+06 Fmax= 1.26050e+05, atom= 9205  
Step= 22, Dmax= 1.9e-01 nm, Epot= -5.03966e+06 Fmax= 5.55995e+04, atom= 9205  
Step= 25, Dmax= 5.8e-02 nm, Epot= -5.05587e+06 Fmax= 5.70279e+04, atom= 9205  
Step= 26, Dmax= 6.9e-02 nm, Epot= -5.06603e+06 Fmax= 4.24640e+04, atom= 9205  
Step= 27, Dmax= 8.3e-02 nm, Epot= -5.07767e+06 Fmax= 1.63888e+05, atom= 9205

step 28: One or more water molecules can not be settled.  
Check for bad contacts and/or reduce the timestep if appropriate.  
Wrote pdb files with previous and current coordinates  
Step= 29, Dmax= 5.0e-02 nm, Epot= -5.08515e+06 Fmax= 2.81433e+04, atom= 9205  
Step= 30, Dmax= 6.0e-02 nm, Epot= -5.10068e+06 Fmax= 3.79215e+04, atom= 9205  
Step= 31, Dmax= 7.2e-02 nm, Epot= -5.11230e+06 Fmax= 6.56359e+04, atom= 9205  
Step= 32, Dmax= 8.6e-02 nm, Epot= -5.12237e+06 Fmax= 5.25851e+04, atom= 9205  
Step= 33, Dmax= 1.0e-01 nm, Epot= -5.13104e+06 Fmax= 1.10335e+05, atom= 9205  
Step= 34, Dmax= 1.2e-01 nm, Epot= -5.14161e+06 Fmax= 4.20119e+04, atom= 9205 …  
Step= 832, Dmax= 1.1e-02 nm, Epot= -5.81777e+06 Fmax= 7.76055e+03, atom= 9284  
Step= 833, Dmax= 1.3e-02 nm, Epot= -5.81778e+06 Fmax= 9.63210e+03, atom= 9284  
Step= 835, Dmax= 7.6e-03 nm, Epot= -5.81830e+06 Fmax= 8.40019e+02, atom= 9303

writing lowest energy coordinates.

Steepest Descents converged to Fmax \< 1000 in 836 steps  
Potential Energy = -5.8182965e+06  
Maximum force = 8.4001923e+02 on atom 9303  
Norm of force = 1.7506589e+01  
Also if i edit my em.mdp with “define= -DFLEXIBLE” what will be the impact and is it rite to do that?  
[em.mdp](https://gromacs.bioexcel.eu/uploads/short-url/fF0qHIdZoDUspCcRbTaAnW8xrzJ.mdp) (1.1 KB)

please suggest. Thanks

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**Author:** ![SP06](https://avatars.discourse-cdn.com/v4/letter/s/ecb155/32.png) [@SP06](https://gromacs.bioexcel.eu/u/SP06)\
**Post date:** [July 14, 2024, 5:47am UTC](https://gromacs.bioexcel.eu/t/step-13-and-step-28-one-or-more-water-molecules-can-not-be-settled/9033/2 "2024-07-14T05:47:45Z")

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Is your issue resolved? If yes, then please tell me how did you resolve this, as I am having same issue.