[gmx-users] Counterions in DNA simulation

[Yu Kay Law]

Dear all,
In learning how to perform MD simulations, I have recently been 
attempting to repeat the work of Martinez et al, JACS 2001, 123, 12279, 
using the ffamber ports, and have found that my sodium counterions have 
essentially resolvated into free solvent, out of the range of the 
solute.  This phenomenon has recurred upon re-randomisation of the 
velocities at 300K.  I would be grateful if someone could shed light 
into how this occurs for long periods of time, and/or be able to explain 
to me how I can constrain the counterion to stay in the vicinity of the 
phosphate groups of the DNA backbone.
thanks,
Yu Kay
-- 
Yu Kay Law
Graduate Student, Biophysics Program
The Ohio State University
c/o Richard F. Celeste Laboratory of Chemistry
120 W 18th Ave, Columbus, OH 43210
Email: ylaw at chemistry.ohio-state.edu
Phone: +1 (614) 292-2695	Fax: +1 (614) 292-1685
Office: Newman and Wolfrom Laboratory, Room 0106
Homepage: http://www.chemistry.ohio-state.edu/~ylaw/