# Re: [AMBER] MMPBSA

From: George Tzotzos <gtzotzos.me.com>
Date: Tue, 13 Mar 2012 18:26:43 +0100

Thanks Aron,

It makes sense. At the same time, the answer was given in the paper I quoted (which I did not read carefully enough).

In this the authors took 150 adjacent snapshots from 3ns production runs. The authors quote that the sample points should be "nearly uncorrelated, since the correlation times for relaxation of effective energy fluctuations (1ps) are shorter than the time-interval (20ps) used for snapshot extraction".

Best regards

George

On Mar 13, 2012, at 6:13 PM, Aron Broom wrote:

> Just to preface, I'm not familiar with the MMPBSA method, but, in general
> if you want to ensure your snapshots or any kind of data are independent,
> you want to ensure that the time between snapshots is greater than the
> decorrelation time for the variable you are interested in. So, basically,
> whatever measure you are interested in (distance, RMSD, I'm not sure) you
> want to calculate the autocorrelation function for that variable, and see
> how many timesteps it takes to decorrelate (want the autocorrelation value
> to drop below 1/e, which is below ~0.368).
>
> ~Aron
>
> On Tue, Mar 13, 2012 at 1:06 PM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> I'm referring to Case et al., 2003 "Insights into Protein–Protein Binding
>> by Binding Free Energy Calculation and Free Energy Decomposition for the
>> Ras–Raf and Ras–RalGDS Complexes" and in particular the the part in which
>> it is stated that "Previous studieshave shown that 100 –
>> 200 snapshots are sufficient to estimate mean values with reasonable
>> precision,62,63 since the error in the mean decreases with the square-root
>> of the number of snapshots, provided that the sample points are
>> independent."
>>
>> My question is how does one ensure that the sample points are independent?
>> I guess the independence of sample points is determined by the interval in
>> the mmpbsa.in file. Am I right in this assumption? If yes, is there a
>> rule of thumb in setting the interval value?
>>
>>
>> George
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>>
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
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Received on Tue Mar 13 2012 - 10:30:04 PDT
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