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I am trying to simulate bulk dimethyl ether with total constraints, both bonds and angles. I am using lincs with constraint = all-angles in *.mdp file in gromacs.

I am attaching the error I encountered while simulating with total constraint.

"Source file: src/gromacs/mdlib/constr.cpp (line 169)

Fatal error:
Too many LINCS warnings (13139)
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

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors"

My dimethyl-ether.itp file looks like

[ moleculetype ]
;name            nrexcl
 DMT              3

[ atoms ]
;   nr  type  resi  res  atom  cgnr     charge      mass       ; qtot   bond_type
     1   os     1   DMT     O    1    -0.419598     16.00000 ; qtot -0.420
     2   c3     1   DMT    CD    2     0.113700     12.01000 ; qtot -0.306
     3   c3     1   DMT    C1    3     0.113700     12.01000 ; qtot -0.192
     4   h1     1   DMT    HD    4     0.032033      1.00800 ; qtot -0.160
     5   h1     1   DMT    H1    5     0.032033      1.00800 ; qtot -0.128
     6   h1     1   DMT    H2    6     0.032033      1.00800 ; qtot -0.096
     7   h1     1   DMT    H3    7     0.032033      1.00800 ; qtot -0.064
     8   h1     1   DMT    H4    8     0.032033      1.00800 ; qtot -0.032
     9   h1     1   DMT    H5    9     0.032033      1.00800 ; qtot 0.000

[ bonds ]
;   ai     aj funct   r             k
     1      2   1    1.4320e-01    2.3832e+05 ;     O - CD     
     1      3   1    1.4320e-01    2.3832e+05 ;     O - C1    
     2      4   1    1.0970e-01    3.1455e+05 ;     CD - HD     
     2      5   1    1.0970e-01    3.1455e+05 ;     CD - H1    
     2      6   1    1.0970e-01    3.1455e+05 ;     CD - H2    
     3      7   1    1.0970e-01    3.1455e+05 ;     C1 - H3    
     3      8   1    1.0970e-01    3.1455e+05 ;     C1 - H4    
     3      9   1    1.0970e-01    3.1455e+05 ;     C1 - H5    

[ pairs ]
;   ai     aj    funct
     2      7      1 ;     CD - H3    
     2      8      1 ;     CD - H4    
     2      9      1 ;     CD - H5    
     3      4      1 ;     C1 - HD     
     3      5      1 ;     C1 - H1    
     3      6      1 ;     C1 - H2    

[ angles ]
;   ai     aj     ak    funct   theta         cth
     1      2      4      1    1.0978e+02    5.2216e+02 ;      O - CD     - H     
     1      2      5      1    1.0978e+02    5.2216e+02 ;      O - CD     - H1    
     1      2      6      1    1.0978e+02    5.2216e+02 ;      O - CD     - H2    
     1      3      7      1    1.0978e+02    5.2216e+02 ;      O - C1     - H3    
     1      3      8      1    1.0978e+02    5.2216e+02 ;      O - C1     - H4    
     1      3      9      1    1.0978e+02    5.2216e+02 ;      O - C1     - H5    
     2      1      3      1    1.1248e+02    5.5480e+02 ;     CD - O      - C1    
     4      2      5      1    1.0846e+02    3.2468e+02 ;     HD - CD      - H1    
     4      2      6      1    1.0846e+02    3.2468e+02 ;     HD - CD      - H2    
     5      2      6      1    1.0846e+02    3.2468e+02 ;     H1 - CD      - H2    
     7      3      8      1    1.0846e+02    3.2468e+02 ;     H3 - C1     - H4    
     7      3      9      1    1.0846e+02    3.2468e+02 ;     H3 - C1     - H5    
     8      3      9      1    1.0846e+02    3.2468e+02 ;     H4 - C1     - H5    

[ dihedrals ] ; propers 
; for gromacs 4.5 or higher, using funct 9
;    i      j      k      l   func   phase     kd      pn
     2      1      3      7      9     0.00   1.41001   3 ;     CD-     O-    C1-    H3
     2      1      3      8      9     0.00   1.41001   3 ;     CD-     O-    C1-    H4
     2      1      3      9      9     0.00   1.41001   3 ;     CD-     O-    C1-    H5
     3      1      2      4      9     0.00   1.41001   3 ;     C1-     O-    CD-    HD
     3      1      2      5      9     0.00   1.41001   3 ;     C1-     O-    CD-    H1
     3      1      2      6      9     0.00   1.41001   3 ;     C1-     O-    CD-    H2 

Do I need to add any other lines in *.itp file?

I would be thankful if someone can shed light on the following error.

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  • $\begingroup$ This error occurs when the velocities are such that some internal coordinate displaces too much from the linear constraint. The typical solution is to reduce the integration time step. $\endgroup$
    – Anon
    Aug 25, 2023 at 12:54
  • 2
    $\begingroup$ @anupama please make a note of the way I formatted the text using code blocks. This makes the post more readable. Please consider using them in your future questions. $\endgroup$ Aug 25, 2023 at 20:05

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