# Re: [AMBER] time correlation function

From: giulia palermo <giulia.palermo83.gmail.com>
Date: Thu, 13 Nov 2014 12:44:52 +0100

Dear Daniel,

thank you for your suggestions. I also have an other question.

Is there a direct way with ptraj or cpptraj to calculate the angle 'tau'
between the principal axis of an alpha-helix and the z-axis of my reference
system (i.e. the cartesian coordinates)??

Moreover, after having calculate the 'tau' angle for an alpha-helix, is it
possible to directly calculate with ptraj/cpptraj the time correlation
function between this angle and the 'tau' angle of an pther alpha-helix??

I have a complex system in which I need to understand how the movements of
one alpha-helix is correlated in time with the movement of an other
alpha-helix. Thus, I thought that the angle between the pricipal axis of
the helices and the z-reference axis could be a suitable metrix.

I also wonder if there are other commands in ptraj that allow to calculate
the helix-tilting that could be an other suitable metrix for solving my
probelm.

Thank you very much
Best regards.

2014-11-12 19:37 GMT+01:00 Daniel Roe <daniel.r.roe.gmail.com>:

> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Nov 13 2014 - 04:00:06 PST
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