On Mon, Dec 29, 2014, Sylvester Tumusiime wrote:
>
> 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?
I'm not sure what Dan (the tutorial author) meant by the term "by default"
here: cpptraj only does an rms fit (and changes the coordinates) if you
have an "rms line" in your script. So, yes, you (generally) need such
a line for actions like atomicfluct and time correlation measurements.
(Dihedrals don't change when the molecule is rotated or translated, so
there it doesn't matter whether you have an rms command or not.)
Thanks for asking the question: we'll update the tutorial to make this
clearer.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Dec 29 2014 - 18:30:03 PST
