[gmx-users] (no subject)

Mark Abraham Mark.Abraham at anu.edu.au
Fri May 8 11:38:41 CEST 2009

Antonia V. wrote:
> Dear all,
> I am trying to simulate a water-liquid crystal system. My initial is box 
> is creating by merging two well equilibrated boxes of water and LC. 
> After a steep simulation of about 1,000,000 steps I try to do an md 
> simulation but I get the error
> "Water molecule starting at atom 9103 can not be settled.
> Check for bad contacts and/or reduce the timestep"
> In order to get the simulation running I have to use a tiny timestep 
> (0.00001).

Have a look at the region around atom 9103 in case you can deduce a 
physical reason for large forces that would make applying constraints 

Otherwise, consider alternative approaches to generating your initial 
structure. It's not clear to me that whatever you mean by "merging" is 


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