AMBER Archive (2003)

Subject: Re: size of a simulation system

From: Pratul Agarwal (pratulka_at_rocketmail.com)
Date: Wed Apr 02 2003 - 08:32:44 CST

> 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?

Folks at Los Alamos have recently simulated the entire ribosomal unit (I think
it had close to a million atoms), but they used a supercomputer for that. So it
depends on the computing resources you have. They used NAMD with AMBER
force-field.

> 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.

Depends on the kinds of motions you are looking for. Are you planning any kind
of principal component analysis?

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