[gmx-users] The sum of the two largest charge group radii is larger than rlist

[pratibha]

Hi all

I would like to first quench my system from 500K to 300K and then do NPT
eqilibration followed by NPT production run. But while running grompp for
NPT eqilibration, I am getting following error :

  The sum of the two largest charge group radii (10.876598) is larger than 
rlist (1.000000)

 My system contains protein, cosolvent and water molecules. I think my mdp
settings are incompatible with the algorithm.
I am using following parameters for quenching :

; Run parameters
integrator      = md            ; leap-frog integrator
nsteps          = 100000        ; 0.002 * 100000 = 200 ps
dt              = 0.002         ; 2 fs
; Output control
cutoff-scheme   = Verlet
nstxout         = 1000          ; save coordinates every 2 ps
nstvout         = 1000          ; save velocities every 2 ps
nstxtcout       = 1000          ; xtc compressed trajectory output every 2
ps
nstenergy       = 1000          ; save energies every 2 ps
nstlog          = 1000          ; update log file every 2 ps
; Bond parameters
;continuation   = yes           ; Restarting after NPT
constraint_algorithm = lincs    ; holonomic constraints
constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter      = 1             ; accuracy of LINCS
lincs_order     = 4             ; also related to accuracy
; Neighborsearching
ns_type         = grid          ; search neighboring grid cells
nstlist         = 5             ; 10 fs
rlist           = 1.0           ; short-range neighborlist cutoff (in nm)
rcoulomb        = 1.0           ; short-range electrostatic cutoff (in nm)
rvdw            = 1.0           ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype     = PME           ; Particle Mesh Ewald for long-range
electrostatics
pme_order       = 4             ; cubic interpolation
fourierspacing  = 0.16          ; grid spacing for FFT
; Temperature coupling is on
tcoupl          = V-rescale     ; modified Berendsen thermostat
tc-grps         = Protein Non-Protein   ; two coupling groups - more
accurate
tau_t           = 0.1   0.1     ; time constant, in ps
ref_t           = 300   300     ; reference temperature, one for each group,
in K
; Pressure coupling is on
pcoupl          = Parrinello-Rahman     ; Pressure coupling on in NPT
pcoupltype      = isotropic     ; uniform scaling of box vectors
tau_p           = 2.0           ; time constant, in ps
ref_p           = 1.0           ; reference pressure, in bar
compressibility = 4.5e-5        ; isothermal compressibility of water,
bar^-1
; Periodic boundary conditions
pbc             = xyz           ; 3-D PBC
; Dispersion correction
DispCorr        = EnerPres      ; account for cut-off vdW scheme
; Velocity generation
gen_vel         = no            ; Velocity generation is off
; Quenching
annealing = single single
annealing_npoints = 21 21
annealing_time = 0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160
170 180 190 200 0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170
180 190 200
annealing_temp = 500 490 480 470 460 450 440 430 420 410 400 390 380 370 360
350 340 330 320 310 300 500 490 480 470 460 450 440 430 420 410 400 390 380
370 360 350 340 330 320 310 300

And for NPT equilibration I am using :

define          = -DPOSRES      ; position restrain the protein
; Run parameters
integrator      = md            ; leap-frog integrator
nsteps          = 50000         ; 2 * 50000 = 100 ps
dt              = 0.002         ; 2 fs
; Output control
nstxout         = 100           ; save coordinates every 0.2 ps
nstvout         = 100           ; save velocities every 0.2 ps
nstenergy       = 100           ; save energies every 0.2 ps
nstlog          = 100           ; update log file every 0.2 ps
; Bond parameters
continuation    = yes           ; Restarting after NVT
constraint_algorithm = lincs    ; holonomic constraints
constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter      = 1             ; accuracy of LINCS
lincs_order     = 4             ; also related to accuracy
; Neighborsearching
ns_type         = grid          ; search neighboring grid cells
nstlist         = 5             ; 10 fs
rlist           = 1.0           ; short-range neighborlist cutoff (in nm)
rcoulomb        = 1.0           ; short-range electrostatic cutoff (in nm)
rvdw            = 1.0           ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype     = PME           ; Particle Mesh Ewald for long-range
electrostatics
pme_order       = 4             ; cubic interpolation
fourierspacing  = 0.16          ; grid spacing for FFT
; Temperature coupling is on
tcoupl          = V-rescale     ; modified Berendsen thermostat
tc-grps         = Protein Non-Protein   ; two coupling groups - more
accurate
tau_t           = 0.1   0.1     ; time constant, in ps
ref_t           = 300   300     ; reference temperature, one for each group,
in K
; Pressure coupling is on
pcoupl          = Parrinello-Rahman     ; Pressure coupling on in NPT
pcoupltype      = isotropic     ; uniform scaling of box vectors
tau_p           = 2.0           ; time constant, in ps
ref_p           = 1.0           ; reference pressure, in bar
compressibility = 4.5e-5        ; isothermal compressibility of water,
bar^-1
refcoord_scaling = com
; Periodic boundary conditions
pbc             = xyz           ; 3-D PBC
; Dispersion correction
DispCorr        = EnerPres      ; account for cut-off vdW scheme
; Velocity generation
gen_vel         = no            ; Velocity generation is off

Please help me correct my mdp files (if required) so that I can accomplish
my task.
Thanks in advance.




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