MD analysis

From: snoze pa (
Date: Mon Apr 17 2006 - 14:37:31 CDT

Hi all,
 In my simulation the final MD structure seems to be slightly moved(tilted
from vertical axis) away from the original minimized structure. First MD was
for 1ns and then for 2ns.
In both situations the final structure is tilted from the original
structure, which is due to a large loop region. I want to analyse my data.
Which one
is proper way
1. Analyse the data based on MD output as it or
2. Analyse the data after overlaping the final MD struture into PDB file
obtained from minimization. In this case I also calculated the rmsd and it
is 1.4.

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