[gmx-users] Re: EM crashes

[Mark Abraham]

On 8/04/2010 5:24 PM, Ozge Engin wrote:
> Hi Ravi,
>
> I had a similar problem to yours when I was dealing with simulation of a
> peptide channel. I had the crystal structure of the channel consisting
> of crystal water molecules and the peptide channel. I energy minimized
> the system. Although nothing seems to be overlap, energy minimization
> crashed. After that I decided to put each water molecule into the
> channel one by one, and did energy minimization after each water
> molecule. If the energy minimization did not crash, I continued adding
> another water molecule. If it crashed I changed the location of the last
> water molecule in the channel. But I am afraid you have much more water
> molecules than mine. I had more or less 100 water molecules within the
> channel, and also note that I had not any ions in the system.

EM can also crash because of voids... if there's a hole, then things 
will tend to fill it, which can lead to a problem elsewhere.

Also, on the ions, consider introducing them after no-ions EM is working 
properly.

Mark