Dear community members, Recently I'm using GMX 5.1.4 to simulate EPM2 CO2 with virtual sites, while I met continual LINCS WARNING. I've been struggling for more than week but make no progress in fixing it.. : (
Here attach my pdb, top, and mdp files below. I would much appreciate any tip & comments. Thanks Pimo ----- ***command used*** gmx_d insert-molecules -f co2EPM2.pdb -ci co2EPM2.pdb -o testco2.pdb -box 5 5 5 -nmol 999 gmx_d grompp -f em.mdp -po testco2em.mdp -c testco2.pdb -p co2EPM2.top -o testco2em.tpr gmx_d mdrun -s testco2em.tpr -deffnm testco2em ***error*** Step 12, time 0.012 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000000, max 0.000000 (between atoms 2201 and 2202) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 21 22 48.5 0.1978 0.1978 0.1978 2496 2497 47.7 0.1978 0.1978 0.1978 2496 2497 47.7 0.1978 0.1978 0.1978 2496 2497 47.7 0.1978 0.1978 0.1978 2496 2497 47.7 0.1978 0.1978 0.1978 ***co2EPM2.pdb*** TITLE CO2 with dummy masses REMARK THIS IS A SIMULATION BOX CRYST1 50.000 50.000 50.000 90.00 90.00 90.00 P 1 1 MODEL 1 ATOM 1 M1 CO2 1 0.171 0.000 0.000 1.00 0.00 ATOM 2 M2 CO2 1 2.149 0.000 0.000 1.00 0.00 ATOM 3 C CO2 1 1.160 0.000 0.000 1.00 0.00 ATOM 4 O1 CO2 1 0.000 0.000 0.000 1.00 0.00 ATOM 5 O2 CO2 1 2.320 0.000 0.000 1.00 0.00 TER ENDMDL ***co2EPM2.top*** [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 no 1.0 1.0 [ atomtypes ] ; type mass charge ptype sigma(nm) epsilon(kJ/M) M 22.00475 0.0000 A 0.00000 0.0000 C 0.00000 0.6512 V 0.27570 0.2339 O 0.00000 -0.3256 V 0.30330 0.6694 [ moleculetype ] ; name nrexcl CO2 2 [ atoms ] ; nr type resnr residu atom cgnr charge mass 1 M 1 CO2 M1 1 0.0000 22.00475 2 M 1 CO2 M2 1 0.0000 22.00475 3 C 1 CO2 C 1 0.6512 0.00000 4 O 1 CO2 O1 1 -0.3256 0.00000 5 O 1 CO2 O2 1 -0.3256 0.00000 [ constraints ] ; ai aj funct distance 1 2 1 0.1978252 [ virtual_sites2 ] ; ai aj ak funct a 3 1 2 1 0.5000 4 1 2 1 1.086376 5 2 1 1 1.086376 [ exclusions ] 3 4 5 4 5 3 5 4 3 [ system ] CO2EPM2 [ molecules ] ; name nmol CO2 1000 ***em.mdp*** define = ; RUN CONTROL PARAMETERS integrator = steep tinit = 0 dt = 0.001 nsteps = -1 init_step = 0 simulation_part = 1 comm-mode = Linear nstcomm = 100 comm-grps = emtol = 10.0 emstep = 0.01 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 energygrps = system cutoff-scheme = Verlet nstlist = 10 ns_type = grid pbc = xyz periodic_molecules = no verlet-buffer-tolerance = -1 rlist = 1.5 rlistlong = -1 nstcalclr = -1 ; Method for doing electrostatics coulombtype = PME coulomb-modifier = Potential-shift-Verlet rcoulomb-switch = 0 rcoulomb = 1.5 ; Relative dielectric constant for the medium and the reaction field epsilon_r = 1 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = Cut-off vdw-modifier = Potential-shift-Verlet ; cut-off lengths rvdw-switch = 0 rvdw = 1.5 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = no ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Separate tables between energy group pairs energygrp-table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order = 4 ewald_rtol = 1e-05 ewald-rtol-lj = 0.001 lj-pme-comb-rule = Geometric ewald_geometry = 3d epsilon_surface = 0 ; Temperature coupling tcoupl = Berendsen nsttcouple = -1 nh-chain-length = 10 print-nose-hoover-chain-variables = no ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau-t = 1 ref-t = 300 ; pressure coupling Pcoupl = no Pcoupltype = anisotropic nstpcouple = -1 tau-p = 0.5 compressibility = 0 0 4.5e-5 0 0 0 ref-p = 0 0 300 0 0 0 refcoord_scaling = No annealing = annealing-npoints = annealing-time = annealing-temp = gen-vel = yes gen-temp = 300 gen-seed = 173529 ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = Lincs continuation = no Shake-SOR = no shake-tol = 0.0001 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 morse = no simulated-tempering = no simulated-tempering-scaling = geometric sim-temp-low = 300 sim-temp-high = 300 swapcoords = no adress = no -- 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.