[gmx-users] LINCS WARNING during EPM2 CO2 Simulation
Mark Abraham
mark.j.abraham at gmail.com
Thu Oct 19 13:21:27 CEST 2017
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 <pimooni at 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
> --
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