On Tue, Aug 21, 2018 at 12:10 PM Robert Molt <rwmolt07.gmail.com> wrote:
> principle component. My last question is not AMBER-specific, I do not
> believe. When I examine the visualization of the "mode" of largest
> variance, I see an extreme lengthening of several bonds in VMD (i.e.,
> they look like they are "stretching" to an unphysical degree). I am very
> confused why this could happen, short of user error. Is it for some
> reason "normal" to see that the highest variance in positions between
> "bonded" atoms could be large, as in visually stretched a huge degree? I
> assume not, and that this is an error somewhere on my part, but I wanted
> to check if I have a misunderstanding before I go back to the drawing board.
This is in fact normal, and is a consequence of projecting your
original structure into "eigenspace". I will attempt to elaborate but
will probably do a poor job, so bear with me.
As you allude to, the eigenvectors that you obtain from PCA represent
the axes which explain variance in your system (in the case of
Cartesian space, it's positional); the eigenvector corresponding to
the largest eigenvalue accounts for the largest variance, the next
eigenvector the second-largest variance, and so on. However, unless
your system is extremely simple, the eigenvectors by themselves do not
necessarily explain any "real" motion - any motion undergone by the
system is a combination of motion along several eigenvectors. This is
why when you isolate just one, things can look strange. You can even
think about this in terms of projecting along the "normal" Cartesian
XYZ axes. Say you have a bond that lies almost primarily along the X
axis. If you project it along either the Y or Z axes it would look
squished.
Hopefully that helps a bit,
-Dan
PS - Another option for viewing motion along eigenvectors you may find
helpful is to use the 'nmwiz' keyword of 'diagmatrix' to generate
output which can be visualized with the 'nmwiz' plugin of VMD.
>
>
> On 8/21/18 9:39 AM, Daniel Roe wrote:
> > Hi,
> >
> > On Mon, Aug 20, 2018 at 10:54 PM Jason Swails <jason.swails.gmail.com> wrote:
> >> You have stripped out residues 1-37 and 319-<total number of residues>.
> >> You now have 244 residues left (it seems that your system doesn't have 318
> >> full residues? I would have expected 281 left if it did). These are now
> >> residues 1-244 since cpptraj always numbers residues from 1.
> > Jason's explanation is spot-on (as usual).
> >
> > Note that in recent versions of CPPTRAJ you can now use the ':;'
> > (colon semicolon) token to use original residue numbers (even after
> > stripping the system), e.g.
> >
> > :;38-318&!.H=
> >
> > This may be more intuitive. Hope this helps,
> >
> > -Dan
> >
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>
> --
> Dr. Robert Molt Jr.
>
>
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Received on Tue Aug 21 2018 - 09:30:02 PDT
