Hi Dan
Thanks for this input!
Yes I am using correl currently to generate NXN maps ( using the byres keyword).
Prior to this I am stripping my mdcrd of any ions/waters/organic solvents....
Thanks
Debarati
From: Daniel Roe<mailto:daniel.r.roe.gmail.com>
Sent: 01 December 2021 08:52
To: AMBER Mailing List<mailto:amber.ambermd.org>
Subject: Re: [AMBER] Dynamic cross correlation matrices in AMBER20
Hi,
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,
-Dan
On Wed, Nov 17, 2021 at 11:50 AM Debarati DasGupta
<debarati_dasgupta.hotmail.com> 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 - 06:30:02 PST
