dear gmx-users, During equilibriation i get the following error.Any suggestions please.
*grompp* WARNING 1 [file npt.mdp]: The sum of the two largest charge group radii (2.369582) is larger than rlist (1.000000) This run will generate roughly 73 Mb of data There was 1 warning Back Off! I just backed up npt.tpr to ./#npt.tpr.5# gcq#113: "I Don't Like Dirt" (The Breeders) * mdrun* WARNING: For the 1498 non-zero entries for table 2 in table_Na_Cl.xvg the forces deviate on average -2147483648% from minus the numerical derivative of the potential WARNING: For the 1498 non-zero entries for table 2 in table_Na_Cl.xvg the forces deviate on average -2147483648% from minus the numerical derivative of the potential Making 1D domain decomposition 2 x 1 x 1 Back Off! I just backed up npt.trr to ./#npt.trr.6# Back Off! I just backed up ener.edr to ./#ener.edr.23# starting mdrun 'NA SODIUM ION in water' 50000 steps, 50.0 ps. step 0: Water molecule starting at atom 6153 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step0b_n1.pdb to ./#step0b_n1.pdb.23# step 0: Water molecule starting at atom 4410 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step0b_n0.pdb to ./#step0b_n0.pdb.23# Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.23# Back Off! I just backed up step0c_n0.pdb to ./#step0c_n0.pdb.23# Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates *Segmentation fault* *mdp file* title = nacl define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 50000 ; 2 * 50000 = 100 ps dt = 0.001 ; 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 = no ; 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 = user energygrps = Na Cl Sol energygrp_table = Na Cl vdwtype= user fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = SOL Na Cl ; two coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = 300 300 300 ; 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 ; Velocity generation gen_vel= yes gen_temp= 300.0 gen_seed= -1
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