Re: Generating a gromacs topology file for analyzing NAMD trajectories

From: patrick wintrode (
Date: Thu Dec 06 2007 - 08:54:25 CST

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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:40 CST