Hi,
You can calculate various types of matrices with cpptraj ('matrix'
command). You can also diagonalize the matrix and optionally write out
nmwiz-compatible output ('diagmatrix' command). Cpptraj can use PSF
and DCD files as well. See the Amber 14 manual for more details.
-Dan
On Tue, Apr 14, 2015 at 8:25 AM, James Starlight <jmsstarlight.gmail.com> wrote:
> Dear Amber users!
>
> I wonder to ask whether someone used VMDs NetworkView plugin for the
> analysis of the biosimulations carried out in Amber? From the tutorial
> I've found that to calculate covariance matrix prior to Networks
> calculations some external programs like CARMA are used which directly
> works with the NAMD-like psf topologies. Are there any other
> possibilities to do the same using amber-like inputs?
>
>
> Thanks!
>
> James
>
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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 Tue Apr 14 2015 - 09:30:02 PDT
