dear gmx-users,<br> During equilibriation i get the following error.Any suggestions please.<br><br><b style="font-family: comic sans ms,sans-serif;">grompp</b><br><br>WARNING 1 [file npt.mdp]:<br> The sum of the two largest charge group radii (2.369582) is larger than<br>
rlist (1.000000)<br><br><br>This run will generate roughly 73 Mb of data<br><br>There was 1 warning<br><br>Back Off! I just backed up npt.tpr to ./#npt.tpr.5#<br><br>gcq#113: "I Don't Like Dirt" (The Breeders)<br>
<br><b><br>mdrun</b><br><br>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<br><br><br>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<br>
<br>Making 1D domain decomposition 2 x 1 x 1<br><br>Back Off! I just backed up npt.trr to ./#npt.trr.6#<br><br>Back Off! I just backed up ener.edr to ./#ener.edr.23#<br>starting mdrun 'NA SODIUM ION in water'<br>50000 steps, 50.0 ps.<br>
<br>step 0: Water molecule starting at atom 6153 can not be settled.<br>Check for bad contacts and/or reduce the timestep if appropriate.<br><br>Back Off! I just backed up step0b_n1.pdb to ./#step0b_n1.pdb.23#<br><br>step 0: Water molecule starting at atom 4410 can not be settled.<br>
Check for bad contacts and/or reduce the timestep if appropriate.<br><br>Back Off! I just backed up step0b_n0.pdb to ./#step0b_n0.pdb.23#<br><br>Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.23#<br><br>Back Off! I just backed up step0c_n0.pdb to ./#step0c_n0.pdb.23#<br>
Wrote pdb files with previous and current coordinates<br>Wrote pdb files with previous and current coordinates<br><b>Segmentation fault</b><br><br><b>mdp file</b><br>title = nacl <br>define = -DPOSRES ; position restrain the protein<br>
; Run parameters<br>integrator = md ; leap-frog integrator<br>nsteps = 50000 ; 2 * 50000 = 100 ps<br>dt = 0.001 ; 2 fs<br>; Output control<br>nstxout = 100 ; save coordinates every 0.2 ps<br>
nstvout = 100 ; save velocities every 0.2 ps<br>nstenergy = 100 ; save energies every 0.2 ps<br>nstlog = 100 ; update log file every 0.2 ps<br>; Bond parameters<br>continuation = no ; Restarting after NVT<br>
constraint_algorithm = lincs ; holonomic constraints<br>constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained<br>lincs_iter = 1 ; accuracy of LINCS<br>lincs_order = 4 ; also related to accuracy<br>
; Neighborsearching<br>ns_type = grid ; search neighboring grid cells<br>nstlist = 5 ; 10 fs<br>rlist = 1.0 ; short-range neighborlist cutoff (in nm)<br>rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)<br>
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)<br>; Electrostatics<br><br>coulombtype = user<br>energygrps = Na Cl Sol<br>energygrp_table = Na Cl<br>vdwtype= user<br><br>fourierspacing = 0.16 ; grid spacing for FFT<br>
; Temperature coupling is on<br>tcoupl = V-rescale ; modified Berendsen thermostat<br>tc-grps = SOL Na Cl ; two coupling groups - more accurate<br>tau_t = 0.1 0.1 0.1 ; time constant, in ps<br>
ref_t = 300 300 300 ; reference temperature, one for each group, in K<br>; Pressure coupling is on<br>pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT<br>pcoupltype = isotropic ; uniform scaling of box vectors<br>
tau_p = 2.0 ; time constant, in ps<br>ref_p = 1.0 ; reference pressure, in bar<br>compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1<br>; Periodic boundary conditions<br>
pbc = xyz ; 3-D PBC<br><br><br>; Velocity generation<br>gen_vel= yes<br>gen_temp= 300.0<br>gen_seed= -1<br><br><br>