AMBER Archive (2004)

Subject: AMBER: LES Simulations

From: Vlad Cojocaru (
Date: Thu Jan 29 2004 - 11:18:14 CST

Dear Amber users,
  I want to run LES simulations on an RNA loop. I have the non-LES
system equilibrated (water + ions ...PME) and I created the LES topology
(starting from the equilibrated non-LES system) file by making 5 copies
of my region. I copied 10 RNA residues so I introdused more negative
charges. The question is: Do I have to add more Na+ in order to
neutralize the new LES system or the neutrality of the system will be
conserved after making the copies?
Thank you very much for answers

Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1327 
home tel: ++49-551-9963204  

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