[gmx-users] LINCS WARNING during EPM2 CO2 Simulation

[Pimo Oni]

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