different counterions for special type of DNA

From: Vlad Cojocaru <Vlad.Cojocaru_at_mpi-bpc.mpg.de>
Date: Thu 26 Sep 2002 14:59:31 +0200

Dear Amber users,
    I am trying to set up some MD runs for parallel stranded DNA. It is
know that the stability of the structure is also dependent on the
counterions (Li+ comparing to Na+). If I would like to set up different
systems using Na+ as counterion and Li+.
    Now the questions are:
  - Is the adding ions by leap enough accurate to see such kind of
differences during an MD?
  - If it is not then could you suggest some other ways of adding the
I would like to thank you in advance for any kind of advice or reference.
Best wishes,

Vlad Cojocaru 
Max Planck Institut for Biophysical Chemistry 
Deparment: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1389 
e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de  
Received on Thu Sep 26 2002 - 05:59:31 PDT
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