Hi,
On Wed, Nov 12, 2014 at 11:04 AM, giulia palermo
<giulia.palermo83.gmail.com> wrote:
> I assume that the principal axis is stored in the second column (0.7802,
> 0.8411, 0.6899 ...).
> Could you please clarify this point?
As stated at the top of the vector output file the vector is stored as
"vx vy vz cx cy cz cx+vx cy+vy cz+vz", so the X Y and Z components of
the principal axis (i.e. the axis with the largest eigenvalue) for
each frame are in the second, third, and 4th columns respectively. The
next 3 columns are the X Y and Z coords of the center of mass of the
atoms in the mask, and the final 3 columns are the sums of each
component.
> Moreover, if I subsequently specify the following command in order to
> obtain the time-correlation between v0 and v1, I do not obtain any output.
>
> analyze timecorr vec1 v0 vec2 v1 tstep 1.0 tcorr 10000.0 out v0_v1.out
I think that 'timecorr' from ptraj can only use vectors that are
marked with the 'corr' keyword. You should use cpptraj instead, which
doesn't have this restriction.
-Dan
PS - The 'timecorr' analysis command calculates autocorrelations using
spherical harmonic averaging, so make sure that's what you want to do.
>
> Do you have any suggestions that can help me in doing this analysis?
>
> Thank you
> Best regards
>
> Giulia
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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 Wed Nov 12 2014 - 11:00:02 PST
