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
