AMBER Archive (2004)

Subject: AMBER: question about LES simulation

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Thu Jan 29 2004 - 10:43:25 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 

-- 
Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1327 
e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
home tel: ++49-551-9963204  

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