sanni at theochem.uni-frankfurt.de
Thu Apr 5 18:53:58 CEST 2007
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
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
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
More information about the gromacs.org_gmx-users