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

David van der Spoel spoel at xray.bmc.uu.se
Fri Aug 16 07:44:56 CEST 2019


Den 2019-08-16 kl. 06:45, skrev 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?

The interaction between the H 5 and the two O 1 and 3 is too strong. Add 
exclusions.
> 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
> 


-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se


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