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

Dr. Vitaly Chaban vvchaban at gmail.com
Mon Apr 7 12:00:52 CEST 2014


do you have your protein as a single charge group?



Dr. Vitaly V. Chaban


On Mon, Apr 7, 2014 at 11:48 AM, pratibha <kapoorpratibha7 at gmail.com> wrote:
> 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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