AMBER Archive (2008)

Subject: Re: AMBER: B-factor calculation from data with different write frequencies

From: Bill Ross (
Date: Wed May 28 2008 - 12:47:28 CDT

> but will I be sacrificing "quality" of the B-factor
> calculation due to reduced MD sampling?

I imagine so, but I'm not an expert on this. Maybe someone else can
comment on how significant a difference the sampling difference makes.
The alternative is to re-run one of your calculations, or possibly
continue your ntwx=250 calculation.

> Also, I have conducted an
> independent simulation of the same molecule with no ligand bound
> (first simulations were with bound ligand) and with ntwx = 250. Will
> I need to select every other frame from this trajectory as well, in
> order to make the data sets comparable?

Yes, or just compare to the ntwx=250 part of the ligand run. I.e. stage 1
would be compare the ntwx=500 (selected/aggregated) joint run to the
ntwx=250 portion of the ligand run, then if they agree, compare 250 to 250

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