Autoionize error: spontaneously quits

From: dora guzman (
Date: Wed Jun 21 2006 - 18:38:51 CDT

I'm experiencing some difficulty with the autoionize function in VMD
1.8.4. I've tried adding ions to a solvated protein (~60K atoms) with a
concentration range of 0.05 to 0.5, and it continuously displays the
following error:

Warning: ion concentration too low, cannot add Cl ions!
Error: failed to add ions from 10 tries
Try decreasing -from and/or -between parameters (which are set
at 5A)
or decreasing ion concentration, or adding more water

I've tried everything it recommends, but continue to get the same error.

The size of the protein is 95 residues, and I've added 20,420 water
molecules. I can't afford to make the water box too large because it
will be more time consuming to equilibrate and the perform SMD.

Any advice would be greatly appreciated.


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