[gmx-users] Regarding too many LINCS warnings for bicarbonate ion

[Apramita Chand]

Dear Gromacs users,
I am trying to use bicarbonate ions in my simulations employing
AMBER99SBILDN ff in GROMACS 5.1.4. For that I've used the antechamber and
acpype utilities to generate the parameters for Bicarbonate with RESP
charges at HF/6-31G* level of theory.
No matter how many times I change or modify the parameters or constraints,
I'm getting LINCS warnings at equilibration level(have tried both NVT and
NPT with same results. The minimization did not show any errors.
What could be the issue? How do I rectify?
Could anyone give me a reference where bicarbonate ion has been simulated
in GROMACS?
Please help,

Yours sincerely,
Apramita


Snippet from my log file:
*******************************************
Removing pbc first time
Pinning threads with an auto-selected logical core stride of 1

Initializing LINear Constraint Solver

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
LINCS: A Linear Constraint Solver for molecular simulations
J. Comp. Chem. 18 (1997) pp. 1463-1472
-------- -------- --- Thank You --- -------- --------

The number of constraints is 4300
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
G. Bussi, D. Donadio and M. Parrinello
Canonical sampling through velocity rescaling
J. Chem. Phys. 126 (2007) pp. 014101
-------- -------- --- Thank You --- -------- --------

There are: 7800 Atoms

Constraining the starting coordinates (step 0)

Constraining the coordinates at t0-dt (step 0)
RMS relative constraint deviation after constraining: 7.16e-07
Initial temperature: 301.871 K

Started mdrun on rank 0 Wed Jul 31 14:09:46 2019
           Step           Time         Lambda
              0        0.00000        0.00000

   Energies (kJ/mol)
           Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
    1.46991e+03    1.01760e+04    2.06368e+02    3.24377e+03    1.71820e+02
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
   -2.97219e+05   -3.76312e+03   -2.01119e+03   -7.08962e+04    3.87811e+04
 Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
    6.09951e-01   -3.19840e+05    2.42973e+04   -2.95542e+05   -2.95542e+05
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
    3.06048e+02   -2.01435e+02   -8.17273e+02    7.28740e-07


-------------------------------------------------------
Program gmx mdrun, VERSION 5.1.4
Source code file:
/home/hsb/Downloads/gromacs-5.1.4/src/gromacs/mdlib/constr.cpp, line: 162

Fatal error:
Too many LINCS warnings (1010)
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 .itp file for bicarbonate ion:
*********************************************************************
[ moleculetype ]
;name            nrexcl
 BIC  3

[ atoms ]
;   nr  type  resi  res  atom  cgnr     charge      mass       ; qtot
bond_type
     1    O     1   BIC    O1    1    -0.854577     16.00000 ; qtot -0.855
     2    C     1   BIC    C1    2     1.094563     12.01000 ; qtot 0.240
     3    O     1   BIC    O2    3    -0.854577     16.00000 ; qtot -0.615
     4   OH     1   BIC    O3    4    -0.752315     16.00000 ; qtot -1.367
     5   HO     1   BIC    H1    5     0.366905      1.00800 ; qtot -1.000

[ bonds ]
;   ai     aj funct   r             k
     1      2   1    1.2183e-01    5.3363e+05 ;     O1 - C1
     2      3   1    1.2183e-01    5.3363e+05 ;     C1 - O2
     2      4   1    1.3640e-01    3.76560e+05 ;     C1 - O3
     4      5   1    9.6000e-02    4.627504e+05 ;     O3 - H1

[ pairs ]
;   ai     aj    funct
     1      5      1 ;     O1 - H1
     3      5      1 ;     O2 - H1

[ angles ]
;   ai     aj     ak    funct   theta         cth
     1      2      3      1    1.3025e+02    6.5220e+02 ;     O1 - C1     -
O2
     1      2      4      1    1.2210e+02    6.3530e+02 ;     O1 - C1     -
O3
     2      4      5      1    1.0655e+02    4.1740e+02 ;     C1 - O3     -
H1
     3      2      4      1    1.2210e+02    6.3530e+02 ;     O2 - C1     -
O3

[ dihedrals ] ; propers
; treated as RBs in GROMACS to use combine multiple AMBER torsions per
quartet
;    i      j      k      l   func    C0         C1         C2         C3
      C4         C5
     1      2      4      5      3   27.19600   -7.94960  -19.24640
 0.00000    0.00000    0.00000 ;     O1-    C1-    O3-    H1
     3      2      4      5      3   27.19600   -7.94960  -19.24640
 0.00000    0.00000    0.00000 ;     O2-    C1-    O3-    H1

[ dihedrals ] ; impropers
; treated as propers in GROMACS to use correct AMBER analytical function
;    i      j      k      l   func   phase     kd      pn
     1      3      2      4      1   180.00   4.60240   2 ;     O1-    O2-
   C1-    O3