how to add ions to a system

From: uma mageshwari (mageshwariuma6_at_gmail.com)
Date: Wed Jan 28 2009 - 03:18:19 CST

hello sir,
          I am running molecular dynamics for protein-dna
complex(nucleosome). In the log file it is mentioned that the total
charge=-150e. I think that i have to add some sodium ions to make my system
neutral.
1.will the addition of sodium ions cause any structural/functional
disturbances?
2.Can u tell me how to add ions to system?
3.Is there any need to include periodic boundary conditions while studying
dynamics in vacuum

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:21:41 CST