AMBER: atomicfluct

From: Andres Palencia <>
Date: Tue, 25 Sep 2007 19:45:50 +0200

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

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,


----- End forwarded message -----

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Sep 26 2007 - 06:07:20 PDT
Custom Search