Re: MMPBSA Question

From: Josh Vermaas (
Date: Thu Sep 22 2022 - 14:15:36 CDT

Hi Kelly,

Would you expect your standard deviation to go down with more
frames/data points? The standard deviation measures in some general
sense how far away a typical measurement is away from the mean of a
measurement. If you took 1000 samples from a gaussian distribution, the
standard deviation would be basically the same as if you took 1,000,000
samples. The standard error of the mean does decrease with increasing
number of samples.

The better question I think is how many actually independent samples you
have in your 5000 DCD frames. CaFE is assuming something like a ~100ps
decorrelation time between frames. Is that enough? No idea, but
technically you want independent samples when calculating a standard error.


On 9/22/22 1:56 PM, Mcguire, Kelly wrote:
> Question about standard deviations with MMPBSA. Should I use millions
> of snapshots for better standard deviations. I ran a 10 nanosecond
> simulation of my protein-peptide complex (2 fs timesteps, saved to dcd
> every 1000 steps). That would be 5,000 frames total in the DCD. I used
> CaFE and NAMD to get my MMPBSA result (single trajectory method). For
> CaFE I used stride 5 for the trajectory so that I would use a frame
> every 10 ps, thus a total of 1,000 frames for the MMPBSA calculation.
> My result is in the attached file. I get -29.3 kcal/mol with a
> standard deviation of 11.5. That's a large standard deviation. But, my
> standard error seems decent (11.5/sqrt(1,000) = 0.37), which appears
> to be what others report for these calculations instead of the
> standard deviation. So is this a good result for a single trajectory
> only using 1,000 frames for the calculation, or do I really still need
> to use millions of frames? Thanks!
> *
> <*3A11431281085317296*401663723798950/download/MMPBSAResults.txt__;JSU!!DZ3fjg!_yU9Ko6sdHZlUdvq78zcZfgrQXILxuElkfj_rrsKGKNAAjLmm1ne44mZs0sgKioHGC4Rbwea414Dld2acveG9Q$>
> Dr. Kelly McGuire
> Herzik Lab - Postdoc
> Chemistry/Biochemistry Department
> Natural Science Building, 4104A, 4106A, 4017

Josh Vermaas
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University

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