[gmx-users] Fwd: LINCS WARNING during EPM2 CO2 Energy Min
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 0.00, max 0.00 (between atoms 2201 and 2202) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 21 22 48.50.1978 0.1978 0.1978 2496 2497 47.70.1978 0.1978 0.1978 2496 2497 47.70.1978 0.1978 0.1978 2496 2497 47.70.1978 0.1978 0.1978 2496 2497 47.70.1978 0.1978 0.1978 ***co2EPM2.pdb*** TITLE CO2 with dummy masses REMARKTHIS IS A SIMULATION BOX CRYST1 50.000 50.000 50.000 90.00 90.00 90.00 P 1 1 MODEL1 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. A 0.0 0. C 0.0 0.6512 V 0.27570 0.2339 O 0.0 -0.3256 V 0.30330 0.6694 [ moleculetype ] ; name nrexcl CO2 2 [ atoms ] ; nr type resnr residu atom cgnr charge mass 1 M1 CO2M1 1 0. 22.00475 2 M1 CO2M2 1 0. 22.00475 3 C1 CO2C1 0.6512 0.0 4 O1 CO2O1 1-0.3256 0.0 5 O1 CO2O2 1-0.3256 0.0 [ 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
[gmx-users] LINCS WARNING during EPM2 CO2 Simulation
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 0.00, max 0.00 (between atoms 2201 and 2202) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 21 22 48.50.1978 0.1978 0.1978 2496 2497 47.70.1978 0.1978 0.1978 2496 2497 47.70.1978 0.1978 0.1978 2496 2497 47.70.1978 0.1978 0.1978 2496 2497 47.70.1978 0.1978 0.1978 ***co2EPM2.pdb*** TITLE CO2 with dummy masses REMARKTHIS IS A SIMULATION BOX CRYST1 50.000 50.000 50.000 90.00 90.00 90.00 P 1 1 MODEL1 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. A 0.0 0. C 0.0 0.6512 V 0.27570 0.2339 O 0.0 -0.3256 V 0.30330 0.6694 [ moleculetype ] ; name nrexcl CO2 2 [ atoms ] ; nr type resnr residu atom cgnr charge mass 1 M1 CO2M1 1 0. 22.00475 2 M1 CO2M2 1 0. 22.00475 3 C1 CO2C1 0.6512 0.0 4 O1 CO2O1 1-0.3256 0.0 5 O1 CO2O2 1-0.3256 0.0 [ 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
