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

From: case <>
Date: Sat, 9 Nov 2013 10:30:32 -0500

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.


AMBER mailing list
Received on Sat Nov 09 2013 - 08:00:02 PST
Custom Search