Hi Sang Min,
The distance from the center of mass is not a proper identifier for
these kinds of calculations. To do this properly, you have to map the
water molecules to specific positions around your peptide, and base
your identifiers on that.
E.g. if you have:
H2O-peptide--OH2 and H2O--peptide-OH2, your identifiers, based on the
shortest distance, interchange, but so does the position w.r.t. the
peptide! This is largely unrelated to the center of mass (and more so
the further you go from it). There's no sense in trying to do NMA like
that.
If you get it right, it'll make a very nice study though.
Best,
Tsjerk
On 4/5/07, Sang-Min Park <[EMAIL PROTECTED]> wrote:
Dear all,
I calculated the eigenvalues and eigenvectors from a small peptide with a
closest water neighboorhood watersurrounding.
To do this I generated a new trajectory with the command "trjorder" to order
the watermolecules in a way so that they are close to the center of mass of
the peptide.
From this new trajectory I took only the subsystem "Peptide+ the first 20
closest water" and generated the Hessian.
When I look at the input-files,needed to generate the matrix I see that one
need only the configuration, a top file and a mdp file. (for grompp). So this
would mean, that gromacs would calculate the Potential (the second derivate
of the potential) from this configuration and then calculate the hessian
matrix. Furthermore I calculated the Hessian at every snapshot of the
trajectory.
I tested if its work right and calculated the hessian matrix from the same
configuration, but only changed 2 watermolecules in their index i. (see the
tables below)
for example:
old configuation new configuration
i coordinates i coord.
.... ....
12 O xO1 yO1 zO1 12 O xO2 yO2 zO2
12 H xH11 yH11 zH11 (change index) 12 H xH21 yH21 zH21
12 H xH12 yH12 zH12 --> 12 H xH22 y22 zH22
... ...
... ...
22 O xO2 yO2 zO2 22 O xO1 yO1 zO1
22 H xH21 yH21 zH21 22 H xH11 yH11 zH11
22 H xH22 yH22 zH22 22 H xH12 yH12 zH12
... ...
... ...
In most cases I got the same eigenvalues and eigenvectors but in some cases
the results were very different.
What could be the reason?
Thank you in advance
Sang Min
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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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