From: Parisa Akhski (
Date: Tue Jul 06 2010 - 09:16:20 CDT

Dear VMD users,

I am using autoionize to neutralize a DNA molecule. I am using the command below as posted on the VMD mailing list to make it only place enough ions to neutralize the system:

autoionize -psf file.psf -pdb file.pdb -is 0.0001

The system net charge before adding ions is -18.9999991446e and after adding ions is -0.999999144592e. Isn't that supposed to be zero after adding ions? Or is it acceptable?

Thanks in advance for your help,