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 - 12:22:55 CST

> For me time passed for molecular dynamic simulation is proportional to
> degrees of liberty of your system. Therefore is not a simple multiplication
> per two.

Good point - pairlist generation is order N^2, so looking
at that component of the time might explain it.

Bill

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