[AMBER] velocity trajectory output

From: Daniel Konstantinovsky <daniel.konstantinovsky.yale.edu>
Date: Mon, 19 Jul 2021 15:53:50 -0400

Hi everyone,

I need accurate velocities to calculate correlation functions. I was
wondering if the velocities written by sander and pmemd take periodic
boundary conditions into account. For example, if a molecule jumps from one
end of the box to the other end because of PBC over an MD step, does the
corresponding velocity include the artifact of jumping across the box in
one step or is that excluded? In other words, does the velocity trajectory
include ridiculously large velocities due to wrapping? If yes, is there a
way to turn that off?

Thank you!
Daniel Konstantinovsky
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Received on Mon Jul 19 2021 - 13:00:02 PDT
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