Re: [AMBER] Problems with RMSF calculations

From: Daniel Roe <>
Date: Mon, 29 Jun 2020 12:02:27 -0400


On Fri, Jun 26, 2020 at 2:49 PM <> wrote:
> I would expect the RMSF calculated using this script to give the average
> RMSF from the two production runs

This isn't correct, and the short explanation is because the RMSF
calculation involves a square root. You can convince yourself of this
by taking a simple set of numbers (like 4 5 3 4) and plug them into
the RMSF formula ( RMSF1234 = sqrt(AvgSumSq - Avg^2), where AvgSumSq
is the average of the sum of squares of the values and Avg is the
average of the values. Then calculate RMSF for the first two and last
two values (call them RMSF12 and RMSF34). You'll see that the average
of RMSF12 and RMSF34 is not RMSF1234. Hope this helps,


> using the input above is not the true average of the two trajectories.
> The attached graph will make it clearer.
> comp_mean.png contains the RMSF calculated using cpptraj for the entire PD1
> and PD2 and for PD1 + PD2. I have also plotted here the mean RMSFs (for 10ns
> chunks) for PD 1 and PD 2 that I calculated using python. Am I using the
> RMSF script incorrectly? I want to calculate the residue-wise fluctuations
> of the Ca atoms of the peptide backbone of my entire simulation (i.e. PD 1
> and 2 combined).
> Thanks a lot in advance for all the help!
> Kartik Lakshmi Rallapalli
> References
> 1.;!!Mih3wA!RkWVHZ9uzYaTsfRwSkKOl8GwVSF_aGB56sRRlI2gEzyf_i_Lj7VJPgwZCZ9m$
> 2.
> 3.;!!Mih3wA!RkWVHZ9uzYaTsfRwSkKOl8GwVSF_aGB56sRRlI2gEzyf_i_Lj7VJPgwZCZ9m$
> 4.
> 5.;!!Mih3wA!RkWVHZ9uzYaTsfRwSkKOl8GwVSF_aGB56sRRlI2gEzyf_i_Lj7VJPgwZCZ9m$
> 6.
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Received on Mon Jun 29 2020 - 09:30:04 PDT
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