Hi Prathiba,
I think you should have a look at the "Functional Mode Analysis" method
from Bert de Groot's lab.
Cheers,
Tsjerk
On Sat, Sep 28, 2013 at 8:13 AM, pratibha kapoor
wrote:
> Dear all users
>
> I would like to calculate pc loadings for various integrated factors in the
> form of foll
Dear all users
I would like to calculate pc loadings for various integrated factors in the
form of following sample table:
Integrated Factors
PC1
PC2
PC3
PC4
PC5
PC6
PC7
PC8
PC9
PC10
Total non polar surface area
0.60
-0.07
-0.76
-0.11
0.08
0.05
-0.16
0.08
-0.01
0.02
Native
Hi Pratibha,
The table is all garbled, and your description insufficiently clear for us
to form a mental picture of what you want, what you've tried to get that,
where it goes wrong, or where you get stuck, and how we can help you on the
right track again.
Cheers,
Tsjerk
On Fri, Sep 27, 2013 a
Dear all gmx users
I would like to calculate pc loadings for various integrated factors in the
form of following sample table:
Integrated factorsPC1PC2PC3 PC4PC5PC6PC7PC8 PC9PC10Total nonpolar surface
area0.60 -0.07-0.76-0.11-0.060.11 0.05-0.160.06-0.02Chain exposed area 0.92
-0.14-0.050.12 0.230.
hi all,
Can we plot RMSF versus atom numbers using eigenvectors of a different
simulation and trajectory of another simulation.
I know we can plot RMSF versus atom numbers using the eigenvectors and
trajectory of a same simulation using g_anaeig
Thanks in advance
--
View this message in contex
On Mon, 13 Aug 2007, Matthias Waegele wrote:
Hello,
I have a question concerning principal component analysis.
In principal component analysis (PCA) it is assumed that the coordinates along
each degree of freedom are Gaussianly distributed. If the data does not follow
a normal distribution, P
Hello,
I have a question concerning principal component analysis.
In principal component analysis (PCA) it is assumed that the coordinates along
each degree of freedom are Gaussianly distributed. If the data does not follow
a normal distribution, PCA may not identify the correct principal modes s
Dear David,
thank you ver much!
As a matter of fact, g_angle (3.3) is working perfectly well! It was a stupid error of mine!!
Sorry for the inconvenience...
Best wishes!
Maki Yoshizawa
Celebrate Yahoo! JAPAN 10th Anniversary
___
gmx-users mailing l
[EMAIL PROTECTED] wrote:
Dear David,
thank you very much for your reply!
Indeed I have used -type dihedral.
Could it be, the problem lies in the [].tpr and [].xtc files? I mean,
which subset of atoms must I choose in those files? (This very part of
the previous discussion was obscure to me!)
Dear David,
thank you very much for your reply!
Indeed I have used -type dihedral.
Could it be, the problem lies in the [].tpr and [].xtc files? I mean, which subset of atoms must I choose in those files? (This very part of the previous discussion was obscure to me!)
Best wishes!
Maki Yoshiza
[EMAIL PROTECTED] wrote:
Hello,
I would like to use PCA analysis in the dihedral space.
Despite having read the topics related to this issue in the GROMACS page
I am not quite sure how to accomplish this :-)
The -or option in the g_angle (version 3.3) seems not to be working. I
am already u
Hello,
I would like to use PCA analysis in the dihedral space.
Despite having read the topics related to this issue in the GROMACS page I am not quite sure how to accomplish this :-)
The -or option in the g_angle (version 3.3) seems not to be working. I am already using an index file as sugested i
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