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
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