[gmx-users] visualizing CONCOORD trayectory

[David van der Spoel]

On Tue, 2005-05-24 at 09:08 +0200, Maik Goette wrote:
> Hi
> 
> Just use VMD in command line with the command: vmd x.gro x.xtc
> You will now see the complete trajectory together with bonds, etc.
> To comment Bert's comment: I wasn't able to load a gro-file into pymol 
> yet...I know, one can use the PDB...but...that's just a 
> workaorund...AND...there ARE VMD-users...;)

For the gro file problem with pymol and rasmol you can make a five line
script (I call this rasgro):

#!/bin/csh -f
set PDB = /tmp/hallo.pdb
editconf -f $1 -o $PDB >& /dev/null
rasmol $PDB
rm -f $PDB


> 
> Regards
> 
> Maik Goette, Dipl. Biol.
> Max Planck Institute for Biophysical Chemistry
> Theoretical & computational biophysics department
> Am Fassberg 11
> 37077 Goettingen
> Germany
> Tel.  : ++49 551 201 2310
> Fax   : ++49 551 201 2302
> Email : mgoette[at]mpi-bpc.mpg.de
>          mgoette2[at]gwdg.de
> WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/
> 
> 
> Ruben Martinez-Buey wrote:
> > Hi all,
> > I have generated a CONCOORD trajectory in xtc format (with all atoms 
> > included) and I want to see it . Since I have no a tpr file to use  as 
> > input for ngmx I cannot see the trayectory. Furthermore, with  VMD  it 
> > can be only visualized as one spot/atom, but I cannot see ribbons, 
> > trace, wireframe, backbone or any other grahical representation. Do you 
> > know how to solve this?
> > Thanks a lot in advance for your kind attention,
> > Bests,
> > Ruben
> > 
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> > .
> > 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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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