FW: [gmx-users] (no subject)
antonia_haha at hotmail.com
Fri May 8 11:55:13 CEST 2009
> 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
> 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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