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

From: Jorden Cabal <jordencabal.gmail.com>
Date: Fri, 11 Sep 2020 19:56:32 +0900

Dear All,
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.

Thank you
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Received on Fri Sep 11 2020 - 04:30:02 PDT
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