no, this isn't correct because Amber does a rigid body best-fit prior
to the RMSD calculation.
On Thu, Jun 21, 2012 at 6:36 PM, Sajeewa Pemasinghe <sajeewasp.gmail.com> wrote:
> Hi all,
>
> This a problem about getting my basics correct. If I have a system of two
> atoms having coordinates (1,1,1) and (2,2,2) and after next step in
> simulation they get transformed to (3,3,3) and (4,4,4) the RMSD is
>
> 1) First get the squares of distances i.e (3*(3-1)^2) =12 & (3*(4-2)^2)=12
>
> 2) Get the mean value of distances i.e (12+12)/2=12
>
> 3) Get the square root of the mean distance sqrt(12)
>
> This the same calculation done by AMBER for RMSD calculations (with respect
> to a given reference structure) isn't it?
>
> Please correct me if I am wrong.
>
> Thank you
>
> Sajeewa
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Received on Thu Jun 21 2012 - 16:00:03 PDT
