Hi,
It's very simple. Just calculate the vector from the center of what
you are centering to where you want it centered, then add that vector
to what is being centered.
F(i) = (T - C) + I(i)
where I(i) and F(i) are the initial and final positions of atom i
respectively, T is the target coordinates vector (i.e. where you want
to go), and C is the current position vector.
-Dan
On Thu, Jan 16, 2020 at 3:47 AM DHEERAJ CHITARA <rs138.iiita.ac.in> wrote:
>
> Dear Amber Users,
>
> What is the formula for centering of molecule in cpptraj18.
> How periodic boundary conditions works with rectangular box and octahedral
> box in amber18.
>
> --
> ----
> Dheeraj
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Received on Thu Jan 16 2020 - 12:30:01 PST
