Re: Generating a gromacs topology file for analyzing NAMD trajectories

From: L. Michel Espinoza-Fonseca (
Date: Thu Dec 06 2007 - 09:11:44 CST

In those cases I usually use either the trace or tube rendering and it
works fine for me. Other types of visualization, such as ribbons or
cartoons usually don't work because they need the whole backbone as an
input (unlike the "trace" one, for instance).

Cheers, Michel

On Dec 6, 2007 3:54 PM, patrick wintrode <> wrote:
> Thanks for the replies. I was able to do PCA using just a pdb file and the
> .trr trajectory.
> Now for another question. I did PCA on just the alpha carbons. When I
> generate a trajectory (of the alpha carbons) along the different components,
> it is displayed in VMD as just a collection of points. I've tried displaying
> as "trace", "tube" and various other options. Anyone know how to get VMD to
> draw connections between the alpha carbons?
> Thanks again.
> Patrick L. Wintrode
> Dept. of Physiology & Biophysics
> Case Western Reserve University
> Cleveland, OH 44106

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