size of a simulation system

From: Wen Li <>
Date: Tue, 1 Apr 2003 10:49:42 -0500 (EST)

Hello everyone,

I am planning to run an MD simulation using Amber7 on a system of an
RNA-RNA complex including a total of 170 nts. With a water box, the
system includes a total of 721918 atoms. Is it practical to run a 5 ns MD
simulation on such a big system? Would the simulation results show any
significant movement as evidenced by some experiments? Do you have any
suggestions to obtain the dynamics of this RNA complex.


Wen Li
Wadsworth Center
Received on Tue Apr 01 2003 - 16:53:00 PST
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