Dear all,
I would like to calculate the rms of a specific water molecule (74) in
a simulation. I am using the command atomicfluct with the following
input:
trajin ../reimage_1bbz_chainA.mdcrd 1 55 1
atomicfluct :74.O
The value of rmsd which I obtain is 20 A, however it is wrong, because
the real is about 1 A, as I calulated with the program VMD. The way I
calulate it in VMD is first, aligning the trajactory (previously
reimaged), and then calculating the rmsd. Should I align the
trajectory previously? Should I use the command rms or runningaverage
in ptraj ?
Does anybody know what I am making wrong?
Thanks a lot in adavance,
Andrés
----- End forwarded message -----
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Sep 26 2007 - 06:07:20 PDT
