[DFTB-Plus-User] MD analysis

[Giovanni La Penna]

> printed the molecule's configurations of every steps. Now I want to draw
> all configurations in this file. I wonder if there is any solution or
> any software to do this automatically since it's impossible to do this
> by hand. 

One possibility is to load the XYZ file
into VMD (Visual Molecular Dynamics):

http://www.ks.uiuc.edu/Research/vmd/

The program is accessible upon registration (likewise
DFTB).
If you have a PDB file (in any configuration) of
the same system (same atomic order and assignment
between PDB and XYZ) it is possible to load
the PDB first and the XYZ later as a trajectory
for the coordinates of the model initially loaded as
a PDB.
Once assignments and trajectory are loaded there
are some analysis tools that can be used, beyond
a mere model view.
A plugin development for DFTB+ within VMD would
be interesting.

Best regards,
           Giovanni

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Giovanni La Penna - National research council (Cnr)
Institute for chemistry of organo-metallic compounds (Iccom)
via Madonna del Piano 10,
I-50019 Sesto Fiorentino, Firenze, Italy
tel.: +39 055 522-5264, fax: +39 055 522-5203
e-mail: glapenna at iccom.cnr.it - http://www.iccom.cnr.it/lapenna
skype: giovannilapenna
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