Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials"

From: 冉挺 <>
Date: Mon, 11 Nov 2013 12:20:16 +0800

I did another 4 * 100 ps simulation. I sampled snapshots every 100 steps
(100 fs). The RMS fluctuation was narrowed a lot and kept stable at the
last 3 * 100 ps, but the average DV/DL value changed. So which
average DV/DL value of the four simulations should I used for integration.

On Saturday, November 9, 2013, case wrote:

> On Sat, Nov 09, 2013, 冉挺 wrote:
> >
> > I did first 100ps TI simulation,and its result is listed here. The "R M
> S
> > F L U C T U A T I O N S" of DV/DL equal 10.2061, which seems much larger
> > than the value given by the AMBER tutorial. So how could I make sure to
> get
> > a smaller RMSD value of DV/DL.
> I'm not sure what one would expect. Note that the estimated uncertainty in
> the mean of DV/DL (which is what you want for error analsyis) can be much
> smaller than the RMS of DV/DL, since in the former case you would divide
> by the square root of number of independent samples you have.
> For example, even if the correlation time of the DV/DL time series were as
> large as 1 ps (which is conservative in most cases), your uncertainty in
> the average of DV/DL would be 10.2/sqrt(100) or about 1 kcal/mol.
> Without know more about your system, its hard to say if the
> RMS fluctuations you cite are a symptom of a problem or not.
> ...dac
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PhD Ting Ran
Molecular-Design &  Drug-Discovery Lab
Laboratory Building A212
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Received on Sun Nov 10 2013 - 20:30:02 PST
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