[gmx-users] hessian_matrix_from_ordered_trajectory

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Apr 5 21:24:02 CEST 2007

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

If you get it right, it'll make a very nice study though.



On 4/5/07, 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
> 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 at 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

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

More information about the gromacs.org_gmx-users mailing list