I am trying to simulate dimethyl -ether molecule constraining all bonds and angles.
I am using lincs constraint solver with constraint = all-angles in *.mdp file for simulation in gromacs.
But I ended up with errors.
"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 "
I am attaching the itp file for details information. I am using gaff parameters for the simulation.
[ 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 more information in the *.itp file
It would be of great help, if someone can comment and shed some light regarding the issues.