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
Received on Thu Sep 26 2002 - 05:59:31 PDT
