With cpptraj V14.01 (latest update) you can use 'modes eigenval <modes
dataset name> out <outfile>' to print out the eigenvalue fraction and
cumulative fraction for each eigenvector to get a sense for how much
each eigenvector contributes to the overall motion. Note this
currently only works correctly when you have eigenvalues, not
frequencies (i.e. with 'covar' matrices, not 'mwcovar' matrices since
for the latter eigenvalues are automatically converted to
frequencies).
Hope this helps,
-Dan
PS - Note that you can print rms fluctuations/total displacement for 1
or more eigenvectors with 'modes fluct' and 'modes displ'
respectively, but the results are printed on a per-atom basis which is
not what you want I think.
On Fri, May 16, 2014 at 10:09 PM, Yip Yew Mun <yipy0005.gmail.com> wrote:
> I understand that in protein MD simulations, the first 2 eigenvectors are usually taken into consideration since it should account for most of the protein’s motions. However, I would like to know how can I plot a graph of Eigenvectors against Positional Fluctuations so as to justify for my simulation that 2 principal components is indeed adequate to account for the protein’s motion?
>
> Thanks.
>
> Regards
> Yip Yew Mun
> Graduate, PhD
> Chemistry and Biological Chemistry
> School of Physical and Mathematical Sciences
> Nanyang Technological University
>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
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 Mon May 19 2014 - 07:30:04 PDT
