AMBER Archive (2003)

Subject: Re: size of a simulation system

From: David A. Case (case_at_scripps.edu)
Date: Tue Apr 01 2003 - 15:44:14 CST

On Tue, Apr 01, 2003, Wen Li 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?

As far as I know, this would be a bigger simulation (by quite a bit) than
anybody has run so far. Are you sure that you cannot look at a smaller
piece of your system? I would recommend getting really comfortable running
and analyzing a system with maybe 5% this number of atoms (say 30,000 or
so); then figure your execution times to be at least 20 times longer for
the bigger system.

This is almost a case of, "if you have to ask, you can't afford it".

..regards...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
==================================================================