# Problem in gmx mdrun -deffnm MD step

**URL:** <https://gromacs.bioexcel.eu/t/problem-in-gmx-mdrun-deffnm-md-step/10258>\
**Category:** User discussions\
**Created:** [September 30, 2024, 9:59am UTC](https://gromacs.bioexcel.eu/t/problem-in-gmx-mdrun-deffnm-md-step/10258 "2024-09-30T09:59:51Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![sayan23us](https://avatars.discourse-cdn.com/v4/letter/s/65b543/32.png) [@sayan23us](https://gromacs.bioexcel.eu/u/sayan23us)\
**Post date:** [September 30, 2024, 9:59am UTC](https://gromacs.bioexcel.eu/t/problem-in-gmx-mdrun-deffnm-md-step/10258/1 "2024-09-30T09:59:51Z")

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GROMACS version:2018  
GROMACS modification:  
After giving the command " gmx mdrun -deffnm MD"  
I am getting the below error  
“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”

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**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [October 1, 2024, 7:40am UTC](https://gromacs.bioexcel.eu/t/problem-in-gmx-mdrun-deffnm-md-step/10258/2 "2024-10-01T07:40:41Z")

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Is the system properly energy minimized?

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**Author:** ![sayan23us](https://avatars.discourse-cdn.com/v4/letter/s/65b543/32.png) [@sayan23us](https://gromacs.bioexcel.eu/u/sayan23us)\
**Post date:** [October 3, 2024, 7:55am UTC](https://gromacs.bioexcel.eu/t/problem-in-gmx-mdrun-deffnm-md-step/10258/3 "2024-10-03T07:55:58Z")

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How can I check that?

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**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [October 3, 2024, 8:02am UTC](https://gromacs.bioexcel.eu/t/problem-in-gmx-mdrun-deffnm-md-step/10258/4 "2024-10-03T08:02:39Z")

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Have you run an energy minimization? Did it converge (not always necessary)? Were there any extremely large (difficult to say what’s extremely large) forces at the end of the energy minimization?