do you have your protein as a single charge group?
Dr. Vitaly V. Chaban On Mon, Apr 7, 2014 at 11:48 AM, pratibha <kapoorpratib...@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. > > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/The-sum-of-the-two-largest-charge-group-radii-is-larger-than-rlist-tp5015690.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? 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