AMBER Archive (2002)

Subject: different counterions for special type of DNA

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Thu Sep 26 2002 - 07:59:31 CDT

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
counterions?
I would like to thank you in advance for any kind of advice or reference.
Best wishes,
vlad 

-- 
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