[gmx-users] Water molecule can not be settled

[Mark Abraham]

Hi,

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.

Mark

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
> 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 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.
>
> Sincerely,
> A Guruge
> --
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