AMBER Archive (2004)

Subject: Re: AMBER: A few questions in the protein unfolding simulations using GB model

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Wed Jan 28 2004 - 12:26:31 CST

> > It is a PC running Linux with two processors. As I repeated the 1 ns
> > simulation a few times, the average time is about 10-11 days for dimer
and
> > about 2 days for monomer. There was no other job running at the same
time. I
> > assume it is probable due to the way GB model treats the solvent
effects on
> > the molecule's surface but I coulndn't give any theoretical
explanations.
>

I would suggest taking a closer look at the detailed timings provided at the
end of the sander output, and running single cpu so as not to confuse
the issue even more with different scaling efficiencies for the systems.

GB certainly doesn't scale linearly, but you're also using a cutoff (perhaps
not a good idea) so it's not be N^2 as someone suggested.
also GB doesn't use a pairlist, so it isn't pairlist generation as Bill
suggested.

run shorter benchmarks to test this, you should get reliable timings
with a 15 minute or so run, no need to run for days.

which amber version is this?

carlos

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