[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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