From: Eliac Brown <eliacbrown.yahoo.com>
Date: Tue, 14 Aug 2012 07:45:13 -0700 (PDT)

Dear All
I was wondering what is the difference between the RMS fitting and the usual fitting command of (center :X-XX mass origin).
The Center command beside it reallocates the atoms into the origin of the box, it does also perform RMS fit (see page 112 AMBERTOOLS 1.4 manual).
So, why I got different answers when I calculated the RMSF per residue with the following jobs:
Job I
trajin 1ns.mdcrd 
atomicfluct out RMSF :1-100 byres

Job II
trajin 1ns.mdcrd  
rms first  :1-100
atomicfluct out RMSF :1-100 byres

Note that the 1ns.mdcrd is already centers in both cases using
center :1-100 mass origin
image origin center

Any kind of explanation would be highly appreciated

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Received on Tue Aug 14 2012 - 08:00:04 PDT
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