Hi Daniel,
actually 'vector principal x' was reporting the Y values for the three
eigenvectors instead .. I processed three eigen vectors using V14.25, the third column (y coordinate of three eigen vectors ) corresponds to the first eigen vector X
12500 -0.5919 0.7107 0.3801 23.4887 -5.6361 9.0608 <== PX-amb14
12500 0.6022 0.0766 0.7946 23.4887 -5.6361 9.0608 <== PY-amb14
12500 0.5357 0.6993 -0.4734 23.4887 -5.6361 9.0608 <== PZ-amb14
12500 0.7107 0.0766 0.6993 23.4887 -5.6361 9.0608 24.1994 -5.5595 9.7600 <== PX-amb12 V12.1
many thanks for this
Fatima
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: Friday, May 01, 2015 5:06 PM
To: AMBER Mailing List
Subject: Re: [AMBER] CPPTRAJ V12.1 principal axis different to V13.22 and V14.25
On Fri, May 1, 2015 at 8:34 AM, CHAMI F. <fatima.chami.durham.ac.uk> wrote:
> why V12.1 is different is it a bug or the code has been improved in latest version
There was a bug in older versions of cpptraj and ptraj where the
'vector principal' command reported incorrect eigenvectors. For
example, 'vector principal x' was reporting the X values for the three
eigenvectors instead of X, Y, and Z of the first eigenvector. As you
note, the behavior was fixed a while back in cpptraj version 13.
-Dan
>
> any help
>
> thanks
> Fatima
>
> my CPPTRAIJ INPUT FILE IS:
> parm ../myos_stripwat-4anew4.prmtop
> trajin ../myos_wat-4anew4_md3-8.mdcrd
> #vector vx :1-155 principal x out myos_wat-4anew4_md3-8_PX-amb12.dat
> #vector vx :1-155 principal x out myos_wat-4anew4_md3-8_PX-amb13.dat
> #vector vx :1-155 principal x out myos_wat-4anew4_md3-8_PX-amb14.dat
> vector vz :1-155 principal z out myos_wat-4anew4_md3-8_PZ-amb14.dat
>
--
-------------------------
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 Fri May 01 2015 - 10:00:04 PDT
