[gmx-users] Water molecule can not be settled
mark.j.abraham at gmail.com
Sun Oct 22 16:45:08 CEST 2017
That's only part of the story. See
http://www.gromacs.org/Documentation/Terminology/Blowing_Up. You are
choosing a step size and pressure coupling algorithm suited only for an
already equilibrated system.
On Sun, 22 Oct 2017 00:09 Amali Guruge <amaligg2010 at gmail.com> wrote:
> Dear Gromacs users,
> 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
> 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 rum.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.
> A Guruge
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