I think that each mode just gets a different color. I don't think the
colors signify anything else.
-Dan
On Sunday, June 5, 2016, Himanshu Joshi <himanshuphy87.gmail.com> wrote:
> One more doubt, I generated nmd file to visualize the PC in vmd using nmwiz
> command
> integrated with diagmatrix. When I load the nmd file in VMD, it uses beta
> coloring method.
> But I don't see the beta factor in the nmd file. As I changes the mode in
> VMD, it changes the color
> with some scheme.
> What the color stands for in the nmd file.
>
> On Mon, Jun 6, 2016 at 12:01 AM Himanshu Joshi <himanshuphy87.gmail.com
> <javascript:;>>
> wrote:
>
> > Thanks for the explanation Daniel, it clears my doubts.
> > I figured out the modes commands for the fraction of the eigen values
> also.
> >
> >
> > On Sun, Jun 5, 2016 at 11:28 PM Daniel Roe <daniel.r.roe.gmail.com
> <javascript:;>> wrote:
> >
> >> On Sat, Jun 4, 2016 at 7:14 AM, Himanshu Joshi <himanshuphy87.gmail.com
> <javascript:;>>
> >> wrote:
> >> > Hello folks,
> >> > I am following the tutorial by Cheatham et al at AMBER15 work shop at
> >> > London to perform PCA of a structure in MD simulation.
> >> > http://www.amber.utah.edu/AMBER-workshop/London-2015/pca/
> >> >
> >> > I extracted the eigenmode data file from the covariance matrix of
> >> > coordinates followed by the projection of the structure along the few
> >> > principle components (PC) using the "projection" command as described
> >> in
> >> > the in above tutorial. If I understand it correctly, it is the dot
> >> product
> >> > of the eigen vector and the coordinates of this frame in Angstrom.
> >> Please
> >> > correct me if it is not true.
> >>
> >> It's true.
> >>
> >> > What does it means that the coordinates
> >> > "match well" with the PC. What the relatively high projection to one
> >> > particular mode reflects, some description would be really helpful.
> >>
> >> I believe you are referring to this sentence:
> >>
> >> 'We can now project the trajectory coordinates along PCs to see how
> >> much the coordinates of each frame "match up" along each principal
> >> component.'
> >>
> >> Perhaps not the best description - all this means is that when you
> >> project coordinates along an eigenvector you're getting a sense for
> >> how far each set of coordinates (i.e. each coordinate frame) has
> >> "traveled along" that eigenvector (maybe that's not the best
> >> explanation either). A "high" projection just means the coordinates
> >> have traveled quite far along that eigenvector. Remember, the
> >> eigenvectors are just defining new coordinate axes for the movement of
> >> atoms. They don't necessarily describe actual paths the atoms take
> >> during the simulation.
> >>
> >> >
> >> > My other question is how do I know how much does the corresponding PC
> >> > contribute to the total motion.
> >>
> >> Check out the 'modes eigenval' analysis command in cpptraj.
> >>
> >> -Dan
> >>
> >> >
> >> > Thank you in advance.
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org <javascript:;>
> >> > 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)
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org <javascript:;>
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > --
> > With Regards
> > Himanshu Joshi
> > Department of Physics
> > IISc Bangalore India
> > 560012
> >
> --
> With Regards
> Himanshu Joshi
> Department of Physics
> IISc Bangalore India
> 560012
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <javascript:;>
> 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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Received on Sun Jun 05 2016 - 13:00:02 PDT
