[gmx-users] water molecule can not be settled, what could be the cause?

[Jian Zou]

Hi all,

My simulation halts, and the log file reads

t = 238.148 ps: Water molecule starting at atom 6051 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with 
previous
and current coordinates

t = 238.150 ps: Water molecule starting at atom 7218 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with 
previous
and current coordinates


I use dt=1fs, T=400K, P=3bar for this simulation.
The initial structure is taken as the final structure of 20ps PR-MD.

I also rerun this simulation, but the same thing happend at almost the same 
time (t=230-240ps).


What could be the cause for the above failure in my simulation?
Box size too small?
Could anybody give me some hint to work this problem out?


Thank you very much for your comment.


Regards,

Jian Zou