Hi,
I think what you might want is the correlation matrix calculation or
'matrix correl'. This calculates matrix entries as:
Mij = (<ri * rj> - <ri><rj>) / sqrt( (<ri^2> - <ri>^2) * (<rj^2> - <rj>^2) )
In order to get meaningful results you should probably RMS-fit your
structures to an average structure first (otherwise translational and
rotational motions will dominate). So to calculate a correlation
matrix for only alpha carbons a typical procedure might go (assuming
you have a previously calculated average reference structure or
something similar):
reference average.rst7
trajin traj.nc
rms reference .CA
matrix correl .CA out matrix_correl_CA.dat
If you would like the output by residue specify the 'byres' keyword in
the 'matrix' command. See section 8.11.1 of the AmberTools 13 manual
for more information on the matrix command. Hope this helps,
-Dan
On Sat, Jun 29, 2013 at 12:44 AM, Baogen Duan <dbaogen.gmail.com> wrote:
> Dear all,
>
> I want to use ptraj program to analyze the correaltion matrix of
> center of mass of partial atoms. what should I do to set the mask to obtain
> it? would you like to give me some help? Thanks
>
> Best wishes
>
> Duan Baogen
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Sat Jun 29 2013 - 16:00:02 PDT
