[gmx-users] Trajectory in text format
David van der Spoel
spoel at xray.bmc.uu.se
Tue Apr 27 09:52:00 CEST 2004
On Fri, 2004-04-23 at 18:05, Anton Feenstra wrote:
> Keta Jones wrote:
> > Dear GROMACS community,
> > I want to write the final output trajectories in
> > text(user readable format).Please help me how to do it
> > ?
> > Actually I want to analysis some H-bond, RDF
> > properties separately.Do I have to write a analysis
> > code for this.
> > Is there any analysis code available for this type of
> > analysis.
> The Gromos trajectory is ascii (don't remember what we call it in Gromacs, sorry),
> and the .gro and .pdb structure file formats can be used as trajectories as well.
> From these it is easy, using e.g. awk, or cut, to get the coordinates only.
It's called g87 and it is not trivial to get the coordinates out because
there are 10 numbers on each line.
It will be easier to write it out as pdb files.
Hbond analysis and RDFs are in gromacs tools.
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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