Hi,
On Mon, Oct 26, 2015 at 5:43 AM, Hadeer ELHabashy
<hadeer.elhabashi.gmail.com> wrote:
> like calculating it for oxygen and calculating it for both oxygen and
> nitrogen .
> atomiccorr :MET.O byatom out atomiccorr_O.out
> atomiccorr :MET.O :ALA.N byatom out atomiccorr_O_N.out
The second command does not have valid syntax for 'atomiccorr' - this
command takes only a single mask. If you want to restrict the mask to
either :MET.O *or* :ALA.N use the mask "or" operator, '|', e.g.
atomiccorr (:MET.O)|(:ALA.N) ...
> I was expecting to get 2 columns one for time step or number of frames and
> one for the averaged correlation function for all o or o and N per frame. I
> wanted to graph this relation of the averaged correlation function per time
> or frames of simulation
Why would you expect to get a correlation function? From the manual:
"For each frame, a motion vector is calculated for each selected atom
from its previous position to its current position. For each pair of
motion vectors Va and Vb, the average correlation between those
vectors is calculated as the average of the dot product of those
vectors over all N frames."
"The value of AvgCorr can range from 1.0 (correlated) to 0.0 (no
correlation) to -1.0 (anti-correlated)."
So what you get (for standard output) are 3 columns, "Atom1" "Atom2"
"Average Correlation". If you specify a gnuplot extension (.gnu) for
your output files instead, you will get a "heat map", where the X
column is "Atom1", the Y column is "Atom2" and the colors are the
values of "Average Correlation".
Hope this clarifies things,
-Dan
>
> However I got an out put file I can not understand and when I plot it I
> thought that something is wrong with the data .
> Would you please clarify it to me?!
>
> Regards
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Oct 29 2015 - 08:00:05 PDT
