Re: [AMBER] Production phase for MMPBSA

From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
Date: Wed, 9 Mar 2016 17:08:21 +0000

On Wed, 9 Mar 2016 02:10:24 -0800
Andy Watkins <andy.watkins2.gmail.com> wrote:

> I suppose I was pricing in some degree of that uncertainty and asking
> the question at the margins, i.e. given that:
>
> 1. even an estimate of your correlation time has some error bars on it
> 2. frames separated by slightly less than the true correlation time
> are not remotely as correlated as frames separated by one tenth of
> the correlation time
>
> at what point does throwing out data become deleterious? (I could
> imagine a heuristic being "once frames are separated by 105% of the
> correlation time as calculated by method A" or some such.)

Assuming your data is uncorrelated you probably want to compute an
estimate for the standard error which is stdev / sqrt(N). Stdev is the
sample standard deviation of your data and N the number of uncorrelated
data points. So you can compute how large N should be to push the
standard error below a desired threshold.

When N is very small you anyway don't have any other choice but
increase your simulation time.

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Received on Wed Mar 09 2016 - 09:30:03 PST
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