Dear Amber users:
I have a question about the RMSD calculation using ptraj. The calculating
RSMD value when I used the nofit keyword is big different from one I did not
used nofit keyword. I want to know what is difference between with and
without nofit keyword. When I should use nofit keyword? In the manual, it is
said that coordinates are not modified if the keyword "nofit" is specified.
I am a little confused about this. I do not know what coordinates are not
modified If the nofit keyword is used and why we should modify the
coordinates in the process of RMSD calculation?
In my case, I want to calculate the RMSD of one residue which is solvated in
the water.
Any suggestions could be greatly appreciated.
Best wishes
Hongbin
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Received on Thu Oct 14 2010 - 17:00:02 PDT
