**From:** Josh Vermaas (*vermaasj_at_msu.edu*)

**Date:** Thu Sep 22 2022 - 14:15:36 CDT

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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.

-Josh

On 9/22/22 1:56 PM, Mcguire, Kelly wrote:

*> Question about standard deviations with MMPBSA. Should I use millions
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*> of snapshots for better standard deviations. I ran a 10 nanosecond
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*> simulation of my protein-peptide complex (2 fs timesteps, saved to dcd
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*> every 1000 steps). That would be 5,000 frames total in the DCD. I used
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*> CaFE and NAMD to get my MMPBSA result (single trajectory method). For
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*> CaFE I used stride 5 for the trajectory so that I would use a frame
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*> every 10 ps, thus a total of 1,000 frames for the MMPBSA calculation.
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*> My result is in the attached file. I get -29.3 kcal/mol with a
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*> standard deviation of 11.5. That's a large standard deviation. But, my
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*> standard error seems decent (11.5/sqrt(1,000) = 0.37), which appears
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*> to be what others report for these calculations instead of the
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*> standard deviation. So is this a good result for a single trajectory
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*> only using 1,000 frames for the calculation, or do I really still need
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*> to use millions of frames? Thanks!
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*>
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*> *
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*>
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*>
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*> <https://urldefense.com/v3/__https://www.researchgate.net/profile/Kelly-Mcguire/post/MMPBSA_Results_Standard_Deviations_and_Standard_Errors/attachment/632a69160c295f1f9ad77097/AS*3A11431281085317296*401663723798950/download/MMPBSAResults.txt__;JSU!!DZ3fjg!_yU9Ko6sdHZlUdvq78zcZfgrQXILxuElkfj_rrsKGKNAAjLmm1ne44mZs0sgKioHGC4Rbwea414Dld2acveG9Q$>
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*>
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*>
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*>
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*> Dr. Kelly McGuire
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*> Herzik Lab - Postdoc
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*> Chemistry/Biochemistry Department
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*> Natural Science Building, 4104A, 4106A, 4017
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-- Josh Vermaas vermaasj_at_msu.edu Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology Michigan State University vermaaslab.github.io

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