[AMBER] Can (cp)ptraj calculate the diffusion of the center of mass?

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From: Jose Borreguero <borreguero.gmail.com>
Date: Thu, 4 Sep 2014 18:59:21 -0400

Dear AMBER users,

I want to calculate the diffusion MSD(t) for the center of mass of atoms
specified by a mask. The option 'average' in the action command 'diffusion'
does a different calculation, which is average the atomic MSD(t). I need to
first average the atomic positions (the center of mass), and then calculate
its diffusion. Is it possible with ptraj or cpptraj?

Thanks in advance,
Jose Borreguero
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Received on Thu Sep 04 2014 - 16:30:02 PDT