[gmx-users] water molecule cannot be settled

[Tsjerk Wassenaar]

Hi Carla,

You may have a water molecule trapped inside your protein. Check the
water molecule with the given atom number in a viewer, together with
your structure. If it is inside, you can try to remove it manually
from the system, editing the structure file and decreasing the amount
of solvent listed in te topology file. If you edit the .gro file, do
mind to decrease the number on the second line (the number of atoms)
by three.

Hope it helps,

Tsjerk

On Tue, Sep 29, 2009 at 11:38 AM, Carla Jamous <carlajamous at gmail.com> wrote:
> Hi,
> I have a problem with water molecules in my system: I'm using Gromacs with
> ffamber94 force-field. During minimization, I have this message:
>
> t = 0.014 ps: Water molecule starting at atom 10045 can not be settled.
> Check for bad contacts and/or reduce the timestep.Wrote pdb files with
> previous and current coordinates
>
> The minimization converged. However, molecular dynamics were stopped.
> I tried minimization with different parameters: Flexible,
> position-restrained, reducing my timestep, etc... and nothing worked.
>
> I also tried one simulation with TIP3P water model and another simulation
> with SPC water model and I still get the same error.
> I tried to access: oldwiki.gromacs.org but access is denied.
>
> Please does anyone have a solution to propose?
>
> Thanks
> Carla
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623