Re: [AMBER] Center of mass, velocity, Momentum calculation

From: David A Case via AMBER <>
Date: Mon, 16 Jan 2023 13:29:47 -0500

On Sun, Jan 15, 2023, Dulal Mondal via AMBER wrote:
>I have a trajectory file (nc file) which contains only position information
>but no velocity information.

>1) How can I calculate the center of mass (COM) of a particular residue

In cpptraj, two linked statements should do the trick:

     vector his64com center :64 # computes the center of mass of residue 64
     writedata his64.crd vectraj his64com trajfmt crd noorigin
         #writes out the center of mass coordinates for residue 64 at each
         # frame of the trajectory to the file his64.crd

>2) How can I calculate momentum?

Without having velocities, you can't get at momenta.

...good luck...dac

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Received on Mon Jan 16 2023 - 11:00:02 PST
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