From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Apr 01 2008 - 22:37:45 CDT

Are you sure the dcd loaded properly? Is that also the only molecule
loaded in VMD (it has to be the top molecule if there are others)?

I'm not sure about VMD crashing though; that would be a better
question for VMD-L (although it will require a lot of specific
details in order for someone to figure it out).

On Mar 31, 2008, at 8:12 AM, Maria Sanchez Farran wrote:

> Hi,
>
>
>
> I am a new user of NAMD and Iíve been following the tutorial.
> Currently, I am trying to do the RMSD analysis of the simulation of
> ubiquitin in a water sphere. I loaded the ubq_ws.psf and
> ubq_ws_eq.dcd files in VMD and typed source rmsd.tcl in the Tk
> console. The file rmsd.dat is created but it has no data in it (0
> kB). I am now a kind of stuck in this part. Also, Iíve realized
> that sometimes after typing source rmsd.tcl in the console and
> pressing enter, the VMD window suddenly closes.
>
> Please, can you help me if you have any idea about why is this
> happening?
>
>
>
> Thank you very much!,
>
>
>
> Maria Antonieta Sanchez
>
>

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