[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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