Re: inquiry regarding AMBER

From: David Case <>
Date: Thu 10 Jan 2002 14:51:54 -0800

On Thu, Jan 10, 2002, xz27 wrote:
> We will run the molecular dynamic simulations on DNA on Linux machines. Could
> you please tell how powerful is AMBER 6/7 for DNA systems. How long it need
> for a 2 ns simulation on a 1.8 GHz Linux machine? Is there any limitation on
> system-size of AMBER on DNA?

It all depends on how big a piece of DNA you wish to simulate....

Very roughly:

For a 25,000 atom system (probably 15-20 base-pairs of duplex DNA), your
machine should require something like 1 sec/MD step.

Thus, for a step size of 2 fs, you will need 1,000,000 steps to get to
2ns, or roughly 12 days of time.

Of course, these are guesses, but should give you a rough estimate. I'm
assuming a solvated simulation, using PME with standard parameters, and
the above times could easily be off by a factor of 2.

System size limit on Amber6 is around 100,000 atoms; this will go away
in Amber7.

...good luck...dac

p.s others on the list may have better estimates....

David A. Case                     |  e-mail:
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            |
Received on Thu Jan 10 2002 - 14:51:54 PST
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