AMBER Archive (2007)

Subject: AMBER: atomicfluct

From: Andres Palencia (andres.palencia_at_biotec.tu-dresden.de)
Date: Tue Sep 25 2007 - 12:45:50 CDT

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_at_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

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