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>
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> wrote:
>
>> On Sat, Jun 4, 2016 at 7:14 AM, Himanshu Joshi <himanshuphy87.gmail.com>
>> 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
>> > 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
>> 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
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Received on Sun Jun 05 2016 - 12:30:02 PDT
