So just to make sure i got this correct, when looking at the cosine content
of the principal components i should look at the whole trajectory? Do i
need to include the initial relaxation in the first few ns of the
production simulation?
If there is a high cosine content for the whole trajectory is there
anything else to be done (if i want to look at the low frequency motions of
the trajectory) except for simulate for longer (i have a very large system
so not the favoured option!)?
As you say it seems that lots of people use PCA on short trajectories, even
of large systems, which to me is confusing
Thanks for any insights you can give
Tom
--On Saturday, January 10, 2009 11:49:18 +0100 Tsjerk Wassenaar
<[email protected]> wrote:
Hi Sanjay,
Imagine yourself zig-zagging along a line from one place to another.
If you look at you're motion (and the variance), you'll find that if
you only look at blocks most of it is explained by the zig-zag and
nicely periodic (no cosine content as in Berk Hess' paper). Good, you
think. But if you look at the whole travel, the most important
contribution is the going from one place to another, and if you look
at you're displacement over time with respect to the mean, that will
give you half a cosine. The fact that results in a block do not fit a
cosine does not take away the fact that you're still in the process of
relaxation. I know it's not what you want to hear, but I've seen it
happen to a complex of >600 residues, where relaxation took more than
30 ns. I also know that people often do PCA on short time
trajectories, but it's not the proper thing to do.
Cheers,
Tsjerk
On Sat, Jan 10, 2009 at 7:34 AM, <[email protected]> wrote:
Hi Tsjerk,
thanks
actually my protein is quite larg (509 aa).i had divided my trajectory in
different part and according to your suggestion i calculated
cosine-content for all, and find that trajectory from 5to15 ns and
18to25ns having cosine value very less about 0.03 in both cases(with and
without ligands), while other combination showing higher values (>0.6).so
i think my system is Ist converges around 5ns and maintaining it up to 15
ns after that it may be few conformational fluctuation occurring and
finally it get stabilized from 18to15ns.may that part 15to18ns trajectory
is transition period between to conformational fluctuation. i have also
calculated temp. and pressure during whole simulation and i find that it
is exact Gaussian between 5to25ns.so my confusion is whether i take my
trajectory for ED analysis is from 5to15 or 18to25 or whole from 5to25,
but 5to25 showing value of cosine >0.6.
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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----------------------
TJ Piggot
[email protected]
University of Bristol, UK.
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