AMBER Archive (2007)

Subject: Re: AMBER: Average absolute value of cross velocity (Rate constant from PMF)

From: David A. Case (case_at_scripps.edu)
Date: Fri Oct 26 2007 - 10:22:40 CDT

On Fri, Oct 26, 2007, Catein Catherine wrote:
>
> I am trying to calculate the rate constant (kTST) from the potential of
> mean force results. Could you please kindly teach me how to calculate the
> average absolute value of cross velocity?

I think you will need to modify the code to do this: project the velocities
onto your reaction coordinate, and then carry out the needed averages. There
is no built-in option to do this, as far as I know.

...good luck...dac

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