VMD-L Mailing List

From: Lambert van Eijck (vaneijck_at_ill.eu)
Date: Thu Jun 07 2007 - 09:55:57 CDT

Hi Axel,

that has solved my problem: first read .psf and then the .dcd.

the graphics is pretty fast.

thanks alot!

Lambert

On Thu, 7 Jun 2007, Axel Kohlmeyer wrote:

> On Thu, 7 Jun 2007, Lambert van Eijck wrote:
>
> LvE> Hi,
>
> hi lambert!
>
> LvE> I installed VMD 1.8.6 (linux) and I don't see my molecule when reading a
> LvE> trajectory. The XYZ arrow shows up and when I do the same for a pdb file
> LvE> it *does* show up. Even the example dcd file from the 'proteins' directory
> LvE> is not shown.
> LvE>
> LvE> I get no error messages and the n.o. atoms and frames is correctly
> LvE> displayed.
>
> can you please tell us exactly the sequence of commands that
> you were executing, so that we can try to reproduce this.
> from your desription so far, one can only guess...
>
> please note, that for VMD to show something reasonable, it needs
> to know the 'structure' of your molecule (which atoms types, residues
> etc). many trajectory file formats do not contain this information,
> but only the coordinate data, one usually first loads a matching
> .psf or equivalent file (.pdb and .xyz do also work, if you delete
> the frames afterwards) and _then_ the .dcd/.trr/.xtc/.trj file.
>
> LvE> I've installed VMD (compiled version) on an intel and amd machine, but
> LvE> both show this problem.
>
> LvE> Because the XYZ axes show up, I doubt whether this is a opelgl
> LvE> problem.
>
> agreed.
>
> LvE>
> LvE> Can anyone help me on this?
>
> we can try.
>
> cheers,
> axel.
>
> LvE>
> LvE> best regards,
> LvE>
> LvE> Lambert
> LvE>
> LvE>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>
>