[gmx-users] (no subject)

Erik Lindahl lindahl at stanford.edu
Sat Mar 9 19:38:48 CET 2002

Atom News wrote:

> I have simulated the protein in water. After 362ps, I got the message:
> Water molecule starting at atom 1094 can not be settled.
> Check for bad contacts and/or reduce the timestep.
> Can you help me? Thanks. 

This happens when an atom in a water molecule moves too fast (i.e. the 
water rotates too much in a timestep.), so the SETTLE algorithm that 
constrains the water bond lengths and angle breaks down. It CAN happen 
just by chance once in a blue moon in very large systems (in that case 
it will probably help if you restart from the last position in your 
trajectory, simply because you'll take a *slightly* different path in 
phase space the next time). Usually it's because your timestep is too 
large though (more than 2-3 ps), or because the water molecule is 
bumping into something.



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