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From: Parisa Akhski (Parisa.Akhshi_at_chem.queensu.ca)
Date: Tue Jul 06 2010 - 09:16:20 CDT
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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,
Parisa
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