[gmx-users] settle problem

[Valentin Gogonea]

Dear Gromacs users,

I am doing simulations on a protein in water. Part of the protein and 
the box is frozen. After a while I get the following message:

t = 0.506 ps: Water molecule starting at atom 28740 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with 
previous and current coordinates

t = 0.510 ps: Water molecule starting at atom 28740 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with 
previous and current coordinates

Is there a way to deal with this. I made the integration step smaller 
(initially was 2 fs) but with no success.

Any input will be appreciated.

Thank you

Valentin