Hi, Simplify things until you identify the problematic part. Eg do one CO2 molecule first.
Mark On Thu, 19 Oct 2017 03:16 Pimo Oni <pimo...@gmail.com> wrote: > 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? 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