AMBER Archive (2003)

Subject: RMSF problem

From: yuan bo (yuanbous_at_yahoo.com)
Date: Sat May 10 2003 - 04:31:27 CDT

Dear amber users
It was often reported from some references that
RMSF(the rms fluctuation from average coordinates) is
a good measure of the flexibility of system and the
rms fluctuations about the time averaged stucture
could be calculated for total atom and backbone as
well as for every residue. How to calculate RMSF? I
only read one command "atomicfluct" from ptraj module
of amber 6 that could compute the atomic positional
fluctuations for all the atoms. Usage as follow:
>atomicfluct [out filename] [mask] [start start] [stop
stop] [offset offset] [byres | byatom | bymask]
[bfactor]
If If "byres" is specified, dump the average
(mass-weighted)for each residue. If "bymask" is
specified, dump the average (mass-weighted) over all
the atoms in the original mask. Are RMSFs for total
atoms and residues calculated using the command with
"bymask" and "byres" options or another command? In
other words, what is used as reference coordinate in
atomic position fluctuation calculation? average
structure? I use the "atomicfluct" command to
calculate of RMSF for total atom and residue. I found
that the longer the simulation period used to
calculate RMSF, the bigger RMSF. There are no constant
trend, why?
Could anybody help me? Thanks
yb

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