AMBER Archive (2004)

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

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Jan 28 2004 - 12:21:10 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.

It could be that there is an order of N^2 cost of the GB
algorithm, or possibly the size of the problem has reached
a threshold whereby swapping is occurring. Do you detect
more disk activity with the larger system?

Are you using MPI?

Bill

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