On Mon, Jul 19, 2021, Daniel Konstantinovsky wrote:
>
>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?
Wrapping is off by default. You have to turn it "on" by setting iwrap=1, but
that should be necessary only in a very few situations. We recommend the
defaults, which use netcdf format for trajectories and restart files, and
leaving iwrap=0. (If you later need to do some imaging for visualization
pruposes, use the command in cpptraj for that purpose.)
That said, I don't think you will get odd velocities if you do set iwrap=1.
But you could run a test to make sure.
...dac
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Received on Mon Jul 19 2021 - 18:30:02 PDT
