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 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 0.00, 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