[gmx-users] check for bad contacts and/or reduce the time step if appropriate

[Mark Abraham]

Hi,

Your system is http://www.gromacs.org/Documentation/Terminology/Blowing_Up,
probably because you have clashes from molecules on one side of the box
running into the ones on the other side because you set the boundaries too
small. Using gmx solvate, gmx insert-molecules and/or gmx genconf are the
easiest approaches for generating solvent boxes.

Mark

On Fri, Feb 13, 2015 at 11:50 AM, Daniele Veclani <danieleveclani at gmail.com>
wrote:

> Dear Gromacs Users,
>
> I am trying to simulate a box with 1000 waters.  The box size are of
> 31,07625 A per side. When I go to do the dynamic simulation (mdrun -s
> 1000w.tpr -c 1000w_1.gro, I use force field opls-aa) comes out this error
> message:
>
> step: XX: Water molecule starting at atom xxx can not be settled
> check for bad contacts and/or reduce the time step if appropriate
> Wrote pdb files with previous and current coordinates
>
> my .mdp file is:
>
> ; 7.3.3 Run Control
> integrator                  = steep
> nsteps                      = 50000
> ; 7.3.5 Energy Minimization
> emtol                         = 1000
> emstep                      = 0.001
> ; 7.3.8 Output Control
> nstxout                        = 100
> nstvout                        = 100
> nstfout                         = 100
> nstlog                           = 1
> nstenergy                     = 1
> energygrps                   = System
> ; 7.3.9 Neighbor Searching
> cutoff-scheme               = Verlet
> verlet-buffer-tolerance   = 0.005
> nstlist                             = 10
> ns_type                         = grid
> pbc                                = xyz
> rlist                                 = 1.2
> ; 7.3.10 Electrostatics
> coulombtype                 = PME
> rcoulomb                       = 1.2
> ; 7.3.11 VdW
> vdwtype                        = cut-off
> rvdw                              = 1.2
> DispCorr                       = Ener
> ; 7.3.13 Ewald
> fourierspacing               = 0.12
> pme_order                    = 4
> ewald_rtol                      = 1e-5
>
> can anyone please let me know what is wrong with my system
>
> Best regards
> Daniele Veclani
> --
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