[MMTK] PDB/XYZ trajectrory to mmtk trajectory

Konrad Hinsen research at khinsen.fastmail.net
Wed Feb 25 07:17:20 UTC 2015


On 24/02/2015 18:59, Matti Ropo wrote:

> I am completely new to both nmoldyn and mmtk, but I notice that one can
> read pdb files with MMTK. Problem is how one can transform those to
> trajectories (and more important is it possible at all).

nMOLDYN comes with a trajectory converter that can handle lots of
formats. I don't know if it handles sequences of XYZ or PDB files,
but it's worth checking first.

If it doesn't, it should be straightforward to write a Python script
using MMTK that does the conversion. The examples for trajectory
handling should provide a good starting point:

 
http://dirac.cnrs-orleans.fr/MMTK/using-mmtk/mmtk-example-scripts/trajectory-handling/

Konrad.
-- 
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Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research AT khinsen DOT fastmail DOT net
http://dirac.cnrs-orleans.fr/~hinsen/
ORCID: http://orcid.org/0000-0003-0330-9428
Twitter: @khinsen
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