# Too many Lincs warning

**URL:** <https://gromacs.bioexcel.eu/t/too-many-lincs-warning/624>\
**Category:** User discussions\
**Created:** [August 5, 2020, 10:18am UTC](https://gromacs.bioexcel.eu/t/too-many-lincs-warning/624 "2020-08-05T10:18:17Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![arnab\_1](https://avatars.discourse-cdn.com/v4/letter/a/0ea827/32.png) [@arnab\_1](https://gromacs.bioexcel.eu/u/arnab_1)\
**Post date:** [August 5, 2020, 10:18am UTC](https://gromacs.bioexcel.eu/t/too-many-lincs-warning/624/1 "2020-08-05T10:18:17Z")

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GROMACS version: 2018.1  
GROMACS modification: No  
I am trying to simulate water and tertiary butanol binary mixture. But in the energy minimization step I found _**Fatal error: Too many lincs warning (1233) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX\_MAXCONSTRWARN to -1, but normally it is better to fix the problem**_.  
My em.mdp file is given below:  
_; minim.mdp - used as input into grompp to generate em.tpr_  
_; Parameters describing what to do, when to stop and what to save_  
_integrator = steep ; Algorithm (steep = steepest descent minimization)_  
_emtol = 100.0 ; Stop minimization when the maximum force \< 1000.0 kJ/mol/nm_  
_emstep = 0.01 ; Minimization step size_  
_nsteps = 10000 ; Maximum number of (minimization) steps to perform_

_; Parameters describing how to find the neighbors of each atom and how to calculate the interactions_  
_nstlist = 1 ; Frequency to update the neighbor list and long range forces_  
_cutoff-scheme = Verlet ; Buffered neighbor searching_  
_ns\_type = grid ; Method to determine neighbor list (simple, grid)_  
_coulombtype = PME ; Treatment of long range electrostatic interactions_  
_rcoulomb = 1.0 ; Short-range electrostatic cut-off_  
_rvdw = 1.0 ; Short-range Van der Waals cut-off_  
_pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions_  
_constraints = allbonds_  
_constraint\_algorithm = lincs_

I am learning md simulation using Gromacs for last couple of months. It will be very helpful if you could give some input in this regard.  
thank you

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**Author:** ![mick](https://avatars.discourse-cdn.com/v4/letter/m/f04885/32.png) [@mick](https://gromacs.bioexcel.eu/u/mick)\
**Post date:** [August 5, 2020, 12:43pm UTC](https://gromacs.bioexcel.eu/t/too-many-lincs-warning/624/2 "2020-08-05T12:43:27Z")

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Quick questions:

What happens if you run just a single butanol molecule? I am wondering if the initial coordinates for your butanol model are the source of your troubles.

Also: why are you restraining all-bonds?

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**Author:** ![arnab\_1](https://avatars.discourse-cdn.com/v4/letter/a/0ea827/32.png) [@arnab\_1](https://gromacs.bioexcel.eu/u/arnab_1)\
**Post date:** [August 5, 2020, 5:43pm UTC](https://gromacs.bioexcel.eu/t/too-many-lincs-warning/624/3 "2020-08-05T17:43:19Z")

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Thank you Mick for your kind concern. Lincs warning is still coming when i run with only teriary butanol molecule. Without restraining the all bonds potential energy has become highly positive after energy minimization. Awaiting for your valuable input.

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [August 5, 2020, 5:58pm UTC](https://gromacs.bioexcel.eu/t/too-many-lincs-warning/624/4 "2020-08-05T17:58:00Z")

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Your observation suggests an unstable topology. How did you parametrize the molecule?

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**Author:** ![arnab\_1](https://avatars.discourse-cdn.com/v4/letter/a/0ea827/32.png) [@arnab\_1](https://gromacs.bioexcel.eu/u/arnab_1)\
**Post date:** [August 6, 2020, 5:09am UTC](https://gromacs.bioexcel.eu/t/too-many-lincs-warning/624/5 "2020-08-06T05:09:23Z")

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Thank you jalemkul. All the force field parameter value i have taken from a paper and using those value i have created topology file.