Dear Amber users,
I have a question regarding the use of rms fitting prior to performing
analyses like dihedral, atomicfluct and correlation.
I read in the amber tutorial 1:
/[1]
http://ambermd.org/tutorials/analysis/tutorial1/
that "by default CPPTRAJ calculates the best-fit RMSD, which means each
structure is rotated and translated so as to minimize the RMSD to the
reference structure (in this case the first frame). As such, the 'rms'
command modifies coordinates for all subsequent commands unless 'nofit' is
specified"
therefore, if i am performing analysis using cpptraj, is it not necessary to
add the rms line. e.g.:
rms ToFirst :1-13&!.H= first out rmsd1.agr mass
prior to analysis since the co-ordinates will be modified again?
Thanks
Silver
References
1.
http://ambermd.org/tutorials/analysis/tutorial1/
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Received on Mon Dec 29 2014 - 13:00:05 PST
