On Thu, 5 Apr 2007 18:53:58 +0200
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
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list.
Use the
www interface or send it to
[EMAIL PROTECTED]
Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
I'm not sure if I understand you correctly :
You generated a configuration file of the 20 nearest water
molecules. That means that the index and identity of the
20 waters can differ in each snapshot, however in the top
file 20 is 20 and names neither numbers don't matter. So
the actual identity should not play a role in for the
production of tpr. No you switch the order of lets say:
water molecule 19 with 20.
When you do this you find different eigenvalues of the
hessian in some cases....correct ?
The dimension of the hessian is Nx3,Nx3, in which you have
i=1,2....Nx3 rows and collums. Each element i has the same
order as in the gro file (1,2....N).
So if you switch a line in the gro the hessian is
different too. Although the hessian will allways be build
up from the same set of numbers...it will simply not be
the same matrix (permutations).
So actually I don't really think this way is a good way to
study the time evolution of the hessian.
Better just take the protein, peptide or wathever without
the water.
Did you check if the trace of the hessian (sum of all
eigen values) is more close to constant ?
Anyway,
Good luck.....
greetings
Jelger
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
