[gmx-users] Fwd: Help on the vector component

[Ankita Naithani]

Hi Tsjerk,

Thanks for the explanation. Yes, so  basically, if I am using calpha atoms
for two systems namely apo and holo (the structure is same with holo having
one extra ligand from apo) and then comparing their eigenvectors, it will
be a sensible comparison? Also, since these components correspond to the
direction of motion associated with a particular eigenvector, will we be
sensible in commenting/discussing about the collapse or emergence of
eigenvector components between the two trajectories with regards to the
atom position on x axis as outputted? For instance, if in Apo a particular
atom has high value of total component but maybe in holo that might have a
lower value, so could we try to analyse it in a component way by commenting
upon the collapse or appearance of motion?

[I might have been extremely confusing here, apologies for that]


Kind regards,

Ankita


On Mon, Nov 25, 2013 at 6:45 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Ankita,
>
> If x, y, z are the components (or loadings), then "total" is sqrt(x**2 +
> y**2 + z**2). They indeed define a direction, corresponding with the
> direction of motion/spread associated with the eigenvector.
>
> To compare eigenvectors, make sure that all frames in all trajectories are
> oriented in the same way, using the same or a similar reference structure
> for fitting. Then you can make a comparison like that.
>
> Cheers,
>
> Tsjerk
>
>
> On Mon, Nov 25, 2013 at 1:00 AM, Ankita Naithani
> <ankitanaithani at gmail.com>wrote:
>
> > Hi Tsjerk,
> >
> > Thank you for your reply. So, basically the numbers are just the xyz
> > components. and the Total is, I quite didn't understand what the total
> > would be? If they are dimensionless, does that mean they are defining a
> > direction? I mean should we say that the total component for instance is
> a
> > measure of the direction of the eigenvector? Also, I was wondering if
> this
> > could be valid to use for comparison between eigenvectors of different
> > trajectories to account for or observe the similarity/dissimilarity
> amongst
> > the two?
> >
> >
> > Kind regards,
> >
> > Ankita
> >
> >
> > On Sun, Nov 24, 2013 at 8:27 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> > wrote:
> >
> > > Hi Ankita,
> > >
> > > I had to check the source for this, but -comp writes out the
> eigenvector
> > as
> > > atom-coordinate components (x,y,z), and the norm of the eigenvector
> part
> > of
> > > the given atom (total). The numbers are dimensionless.
> > >
> > > Hope it helps,
> > >
> > > Tsjerk
> > >
> > >
> > > On Sun, Nov 24, 2013 at 2:38 PM, Ankita Naithani
> > > <ankitanaithani at gmail.com>wrote:
> > >
> > > > Hi,
> > > >
> > > > I wanted some help regarding vector components. I.e. when we use the
> > > > g_anaeig command with a flag of -comp, it outputs a file of the
> > > > corresponding eigenvector per atom. So, the x-axis has the atom
> number
> > > and
> > > > the Y-axis has the total, x, y and z components. I am not sure about
> > what
> > > > do they mean? Also, what are the units of these components? Like the
> > > > numbers on Y-axis, what are the corresponding units? I would be
> really
> > > > grateful if anyone could kindly help me on this.
> > > > Apologies for reposting but was wondering if anyone has any thoughts
> on
> > > it?
> > > >
> > > > Best wishes,
> > > >
> > > > --
> > > > Ankita Naithani
> > > >
> > > >
> > > >
> > > > --
> > > > Ankita Naithani
> > > > --
> > > > Gromacs Users mailing list
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> > >
> > > --
> > > Tsjerk A. Wassenaar, Ph.D.
> > > --
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> >
> >
> > --
> > Ankita Naithani
> > --
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
> Gromacs Users mailing list
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-- 
Ankita Naithani