FW: [gmx-users] (no subject)

[Antonia V.]

> Date: Fri, 8 May 2009 19:38:41 +1000
> From: Mark.Abraham at anu.edu.au
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] (no subject)
> 
> 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 
> difficult.
> 
> Otherwise, consider alternative approaches to generating your initial 
> structure. It's not clear to me that whatever you mean by "merging" is 
> reasonable.
> 
> Mark
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