AMBER Archive (2003)

Subject: Re: size of a simulation system

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Wed Apr 02 2003 - 12:37:40 CST

Hi Pratul,

Do you have the reference on that, an article, a web link?

Thanks,
Ioana

On Wed, 2 Apr 2003, Pratul Agarwal wrote:

> > 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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