H.J.Risselada at rug.nl
Thu Apr 5 21:47:09 CEST 2007
On Thu, 5 Apr 2007 18:53:58 +0200
Sang-Min Park <sanni at theochem.uni-frankfurt.de> 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
> 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
> 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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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
Did you check if the trace of the hessian (sum of all
eigen values) is more close to constant ?
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