Re: [AMBER] Dynamic cross correlation between the center of mass of two groups of atoms

From: David A Case <>
Date: Fri, 11 Sep 2020 14:22:32 -0400

On Fri, Sep 11, 2020, Jorden Cabal wrote:

>I want to calculate cross-correlation between the center of mass of two
>different groups of atoms. I understand the process and have successfully
>calculated for all the atoms in my system using the "matrix" command.
>Although I can write a time series data of vectors of COM of the groups I
>am interested in, and then can use my own external code to calculate the
>correlation values, but I want to do it using the "cpptraj" if possible.
>I do not understand how I can mask the center of mass of two groups on the
>run under the "matrix" command in the "cpptraj". Please suggest.

Here's an example that might help:

In this example, the "groups of atoms" are individual residues, but you
can modify the atom selection masks to group atoms however you want.

...hope this helps....dac

AMBER mailing list
Received on Fri Sep 11 2020 - 11:30:03 PDT
Custom Search