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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.