[gmx-users] hessian_matrix_from_ordered_trajectory

Sang-Min Park sanni at theochem.uni-frankfurt.de
Thu Apr 5 18:53:58 CEST 2007

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                                            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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