Dear All,
My system contains water molecules and polyethylene glycol molecules. I generated the box (15.2*15.2*15.2 nm*3) using genbox command. Thereafter, PEG molecules were added using gmx insert-molecules and solvated with gmx solvate.
When I tried to run md, I got the following error.
step 1802: Water molecule starting at atom 93528 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Segmentation fault (core dumped)
my run.mdp file contains following parameters.
integrator = md dt = 0.005 nsteps = 1000000 comm_mode = linear ; nstxout = 500000 nstlog = 1000 nstenergy = 50 nstxtcout = 10000 ; cutoff-scheme = Verlet nstlist = 10 ns_type = grid pbc = xyz rlist = 1.4 ; coulombtype = PME rcoulomb = 1.4 epsilon_r = 1 rvdw = 1.4 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 DispCorr = EnerPres ; Tcoupl = v-rescale tc-grps = System tau_t = .1 ref_t = 298 ; Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 ; gen_vel = no ; constraints = all-bonds constraint_algorithm = lincs lincs_order = 8
Can anyone help me to solve the error. The most of the people commented previously that this error is due to a bad starting structure. If it is the reason, how can I correct it.
Thank you.
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