[gmx-users] water molecule cannot be settled
carlajamous at gmail.com
Tue Sep 29 13:52:25 CEST 2009
Thank you for your reply,
but none of the water molecules with error messages is trapped inside my
protein, nor is it in contact with the protein or the ions in my system.
On Tue, Sep 29, 2009 at 1:15 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> 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,
> On Tue, Sep 29, 2009 at 11:38 AM, Carla Jamous <carlajamous at gmail.com>
> > Hi,
> > I have a problem with water molecules in my system: I'm using Gromacs
> > 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
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