Re: [AMBER] Dynamic cross correlation matrices in AMBER20

From: Daniel Roe <>
Date: Wed, 1 Dec 2021 08:52:19 -0500


You want the 'correl' keyword for the 'matrix' action in cpptraj. (I
guess I should make 'dccm' an alias for that...)

From the manual entry for the 'matrix' action:
 Calculate a matrix of the specified type from input coordinates.
    dist: Distance matrix (default).
    correl: Correlation matrix (aka dynamic cross correlation).

Hope this helps,


On Wed, Nov 17, 2021 at 11:50 AM Debarati DasGupta
<> wrote:
> “Extracting dynamical pairwise correlations and identifying key residues from large molecular dynamics trajectories or normal-mode analysis of coarse-grained models are important for explaining various processes like ligand binding, mutational effects, and long-distance interactions”…
> In these lines a reviewer asked me to check if I can calculate the cross correlation matrices in my CoV2 main protease (residue NXN maps) and check if there is any allosteric motion…
> I am not too sure but I would want to analyze my cosolvents simulation trajectories and plot these cross correlations…
> Is there a way Cpptraj can make this task doable?
> I am using AMBER20
> Thanks all in advance.
> Debarati
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Received on Wed Dec 01 2021 - 06:00:04 PST
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